Separation
by SuicidalImbecile
Summary: Trinity/Neo AU. Neo and Trinity are separated from each other by the council and try doing everything they can to get back together all in the middle of the war. T-M rating. Complete!
1. Chapter 1

Okay, so this is my first Matrix fan fic (that i ever put up and that wasn't terribly bad...I think anyways) and I'd love your advice and such. Constructive criticism please. If you have any complaints or comments, don't be horribly rude. I accept bad reviews but only if you aren't a jerk. Anyway, I really hope you guys like it!

Oh yes, I don't own anything here. Warner, Wachowski, Copyrights. yada, yada, yada- You all get it.

Neo woke in pitch blackness. He was sitting up; now afraid he had woken the love of his life, Trinity, for the fourth time this week. Although it wasn't _his_ fault… he couldn't control the dreams he had. He looked over at Trinity. He obviously hadn't woken her if she kept her soft, even breathing; unlike Neo's fast and heavy breaths. _Well, since I'm up…_ he thought as he carefully lifted himself over Trinity and stepped onto the cold, metal ground. He walked across the room to the crib where his young daughter started to cry. He lifted up the girl and lightly bounced her, hushing her at the same time. Neo realized that his second-long yelp and the darkness of the room had woken the light sleeper up. He couldn't blame her for waking up for she was only a one and a half years old. He turned on a faint light that produced a soft blue glow that seemed to have calmed the baby down. After several minutes, she was fast asleep just like she had been before. He set her back down in the crib and carefully turned the wheel on the door, trying to be as silent as possible. He leaned against the closed door for a minute, squeezing his eyes shut. He covered his eyes with his hands, rubbing them awake, thinking about the dream he had –his lover and child's death caused by the machines of the war. Neo sighed and stood up straight, heading towards the mess hall.

He grabbed a mug from the cabinet and held it under the faucet, waiting for the clear liquid to come out. He went to sit down at the table when the wheel of the door squeaked and spun open. Trinity walked through the door with their baby cuddling with her light blue shirt against her chest. She greeted him with a 'hi' and he returned it with a smile that quickly faded. He was obviously still too upset to talk… even with her. Neo set the mug down onto the table and took the baby from Trinity as she reached into the back of one cabinet to reach for the dry baby formula. While she was mixing the formula with warm water, Neo was holding the baby on his lap, mindlessly playing her dark hair while thinking of a way to tell Trinity about his nightmare. He had decided that even if he didn't _want_ to talk much about it, she could only help him feel better. And of course, she did. He had told her the story: the machines were after him, her, and the baby. Trinity was running behind Neo with the child when the sentinels caught up to them and took Trinity and the baby with their metallic tentacles, but left Neo to run. Except what frightened him the most was that he had not seen what happened to them. He had only heard their screams as they were being taken away.

When he had finished telling her about the dream, she wiped the worried look off her face to put on a reassuring smile. "Neo," she said to him using her quiet but confident voice. "You have to stop worrying yourself. Lily and I will be fine." Neo only nodded and looked down at Lily on his lap.

- - - -

He had never truly known their reason to name the baby Lily. While Trinity was pregnant, they hadn't been sure of what names would suit their daughter –or son for as little as they had known at the time. But when the doctor had told them it was a girl and cleaned her up, wrapped her in a faded pink blanket and handed her to Trinity, she looked into the baby's bright blue eyes she whispered 'Lily' and they decided on that.

Neo had never expected to have children –or child for now…- but he or anyone else ever dared to call Lily a 'mistake' or an 'accident'. Truthfully, he had been terrified of what would happen to him, Trinity, and the baby until the council had agreed to let all three be aboard the ship after Lily and Trinity were settled in Zion for at _least_ three months.

It had come as a surprise to everyone when they found out she was pregnant. First of all, Neo wasn't one hundred percent sure if they could conceive or not and no matter how close they were, he never felt comfortable asking her questions like those. He still remembered exactly how she told him the news, too. It was several days after they left Zion. Apparently, Trinity had taken some home-pregnancy tests from Cas, one of their close friends and also a mother of two children-Dozer's children. She had decided to use them on the ship soon… when she had enough courage. Neo noticed Trinity had been acting strangely. When he had asked her about it, she had simply stated that it was nothing and would kiss him gently on his lips. Neo hadn't been convinced but he trusted her enough to believe what she had told him. The following day they had changed in their room. Trinity went to the bathrooms to take a shower as she figured it would be enough time for the pregnancy test to work.

He clearly remembered her walking back into the room. She couldn't hide her emotions this time. Neo could see the look on her face –the sad, fearful look that broke his heart. He didn't immediately ask her what was wrong but instead stood from the bed and walked over to hug her tightly. He rubbed her back in soothing circular motions as he asked her what was wrong. Not five seconds later, his undershirt was wet with her tears. Suddenly feeling like the worst man alive by making her cry like that, he continued rubbing her back but now started to hush her and whisper to her. "It's okay, Trin," he would say. Her sobs quieted down and she then pulled back just far enough so she could see his face. She shook her head so lightly, she wasn't even sure if he could see it. But she went on. Her voice cracked as she started speaking but she knew he would have to find out sooner or later.

"Umm… Neo… I" _This is a lot worse than I thought._ "I'm pregnant… Neo." She bit down on her lip. This was a well known habit of hers when she was nervous. She felt the calm rubbing on her back stop. Trinity was so nervous she held her breath until Neo showed one sign that he hadn't been petrified right there. For just another moment, Neo was silent. He had then taken a deep breath and spoke to her. "Oh. Well, umm." He paused for a moment then spoke more confidently. "We'll get through it. Don't worry. We'll get through it." He repeated. He took her hands and led her to the bed. They both lied down together, Trinity still crying silently. Neo still held her hand but let the other slide up to her burning cheeks. Lifting his head, he pressed his lips softly against hers. He had purposefully kept theirs together longer than necessary in attempt to help her know he was truly okay with it. It worked, for the most part, and she calmed down a lot. He lifted his lips from hers and touched the skin from beneath her undershirt. He put his lips to the skin right above her belly button. He kissed her stomach in such a way that they both knew Neo wanted to have a baby more than anyone else did.

- - - -

As Neo was still deep in his thoughts, he started to think about the slowness in the Matrix. They haven't had any word from the Oracle, meaning they couldn't do anything to help end the war. Of course, they still had gone into the Matrix a few times a week to keep things under control with agents and to keep their eyes locked on one particular person who may be ready to be unplugged. Aside from the fact that the ending of the war wasn't being helped, days off from the Matrix were always relieving; especially for Neo and Trinity. They had known it was awful to leave Lily with their operator while he had to focus on the three of them in the Matrix. Usually they weren't in for too long but when they were, it wasn't good. But they could easily make it up to Lily by simply playing with her for just a few minutes. Neo was still organizing his thoughts when he was interrupted.

"_Neo._" He looked up, surprised by the tone of Trinity's voice. It wasn't urgent or irritated nor was it calm, but somewhere in between all three. He had then realized that Lily's bottle was ready to be fed to her. He didn't know how many times she had said his name before he answered with a low 'sorry'.

The room was silent –with little interruptions from Lily's cooing in between her sips of formula- until Morpheus came in.

"You three are up early." Morpheus said.

Trinity looked up at Morpheus, fixing himself breakfast at the counter and replied by only saying "Likewise."

Morpheus heard the coldness in her voice, and by her tone he decided to say nothing else. As he walked back to the metal table and benches with his bowl and spork, he smiled back at Lily and took a seat at the other end of the bench Trinity was sitting on. He had begun chewing on his food when he thought of the news he had received just a half hour before. After he swallowed, he spoke up. "We'll be arriving in Zion about four hours from now. The council has to speak to you." Neo immediately looked up to see who he was talking to but only found Morpheus to be looking down into his food and Trinity wondering the same thing as Neo.

"And by 'you', you mean…?" he asked.

"Both of you actually."

"What? Why?" asked Trinity, just as confused as Neo was.

"Not sure." And at that Morpheus left it. He got up, washed his dishes, and exited the other way, fast enough so that by the time they had something to say he would already be out of the room.

**A/N:** (...again...yeah, you'll be seeing a lot of these!) Continued? Yes it is. Please review. It always makes my day (and makes me all happy and fuzzy inside!) and when I'm warm and fuzzy, it makes me want to upload again. Plus, it puts me in a good mood.


	2. Chapter 2

A/N: Writing at three in the morning is not a good idea. Although if I didn't do it now, I never would've. So here you go. Reviews are nice, if you can!**  
**--

Trinity sighed then looked down at Lily. Neo followed her gaze and saw that she had fallen asleep. Trinity got up, took the empty bottle from the table top, and went to the sink to wash it. "I'll put Lily in her crib," said Neo. Trinity looked back and nodded in approval then went back to finishing scrubbing the plastic.

The door was open as Trinity walked through. Lily was in her crib fast asleep and her and Neo's duffel bags were lying on the bed waiting to be packed. Neo wasn't in the room with them though. _Where is he?_ she wondered. Standing in the middle of the room, she shuddered at the coldness of the ship as if she had just felt the temperature drop drastically. Giving one last look at Lily, she started down the hall to where she heard a quiet thud.

There she had found Neo in his old room, the one he had before they had decided to share, which now felt like such a long time ago. He hadn't yet noticed her leaning against the doorway but she enjoyed that. She liked watching him without his knowledge. She liked to see him show affection to the people and things around him when she wasn't there (that he knew of). She liked watching _him_.

She wasn't sure what he was doing but continued to watch and hopefully find out. He untucked the sheets from the bed and folded them neatly on top of the mattress. As he turned, he saw a figure out of the corner of his eye and jumped at the sight.

"You scared me."

"Sorry," she said. "What're you doing, anyways?"

"Oh. Right." He looked down at the sheets folded on the mattress. "It's cold. Well, obviously. I was getting a couple extra blankets for us until Zion can fix the heaters- which I'm sure they won't do this visit."

"Oh. Thank you." She smiled. Neo nodded.

Trinity headed back to their room, Neo following with the two extra sheets in his hands.

Closing the door with his foot, Neo laid the sheets down on their bed and reached into the dresser for both their clothes. Packing silently, both deep in thoughts, they wondered what the council wanted from them. They rarely saw Neo or Trinity except when the news of Neo being the One came and when they announced Trinity was pregnant. Checking the clock, Trinity had realized Neo's shift was soon to begin.

"Neo, it's your shift," she told him.

"Oh!" He was surprised that nearly twenty minutes had passed since they started packing and he wasn't even finished. "Thanks for reminding me," he said to her. Kissing her briefly on the cheek, he left and went down to the lower level of the ship to watch the matrix code for the next two hours.

--

Arriving in Zion had always been delightful. It was good to take a break from the metallic, cold ship once in a while. Except this time, Trinity really didn't want to stay in Zion. This council meeting with her and Neo sounded nothing but bad. Though she couldn't be sure, she tried to ignore her senses and tell herself the council just wanted to congratulate them on a job well done aboard ship, but she couldn't convince herself that was the case.

Link had agreed that he and Zee would take care of Lily while they were at the meeting. Dropping their bags off at their room, Trinity and Neo set off to one of the smaller council rooms.

Entering the room, their fingers entwined, several councilors gave them disapproving looks which caused them to drop their hands back down to their own sides.

"Trinity, Neo, thank you for joining us." Councilor Abigail was the first to speak. The two nodded their heads as they took their place at the table and chairs for the couple.

"To start, we would like to make you aware that we are proud of you two for being able to handle a child on board a ship. It mustn't be easy," the Councilor continued. "To get to my point, Neo, the rest of the Council and I have been monitoring your progress inside the matrix. Unfortunately, we have not seen much. No contact from the Oracle has been confirmed." She paused and Trinity took the opportunity to speak.

"Excuse me, Councilor, but I don't believe that it at Neo's fault. The Oracle will contact him when she feels it is the right time."

"We are well aware of that, Trinity," Councilor West said. "Let us continue." She shut her mouth and quietly sighed, able for only Neo to hear.

Councilor Abigail picked up from where she was interrupted. "The Council believes that your child, Lily, is creating a distraction for Neo's focus on missions aboard ship, therefore, Trinity and Lily shall be temporarily removed from the Nebuchadnezzar." Looking up immediately, Neo had a perturbed look smeared over his usually stoic face.

"_What?_" he asked in disbelief.

Unable to remain calm, Trinity pounded her fist into the table that sat before them. "That's _fucked_!" she nearly yelled causing Neo to shudder.

"Trinity…" Councilor Hamann warned. "We are only doing what we feel is best."

"Why?" Neo whispered to himself, Trinity, and the twelve councilors.

"Excuse me?" asked one of them.

"Why would our daughter be a distraction to me? She and Trinity have nothing to do with this. It isn't _their_ fault _I_ don't know what to do."

A woman whom Neo did not know spoke. "Neo, please, we will keep this temporary. If we think you are making more progress this way, it shall remain the same, if not, we will be sure to have Trinity and Lily placed back on the Nebuchadnezzar as soon as we can."

With tears blurring her vision, Trinity shook her head in disgust and stormed out of the room, slamming the door closed. Outside, she leaned against the wall taking deep breaths. Tears were dropping from the corners of her closed eyes. She heard three loud bangs, knowing that the meeting was over.

Neo stepped out and softly closed the door. Walking over, he took his place against the wall next to Trinity.

"I… don't believe this…" he said, then sighed.

Trinity took his hand from his pocket and locked their fingers together. "I know."

"Yeah, but at least you'll have Lily here. I won't have you or her." His voice cracked when he spoke the last sentence.

Bouncing herself off the wall, she stood in front of Neo with her arms now around his waist and her face in his chest. Trinity was crying now. "I love you. I don't want you to go," she whispered.

Neo couldn't speak. He only stroked her hair and kissed the top of her head.

And there the separated couple hugged. Savoring the feeling now, for they would only have two more days to remember each other completely.


	3. Chapter 3

**A/N:** Chapter 3! Yay. Well, aside from the fact that it sucked, I was very happy to write this.  
Oh yeah, this chapter has a little sex scene in it. If that ain't your cup of tea, you can skip over this chapter as nothing else really goes on in it. Sorry if it's bad, it's the first one I've ever written! X-X Thank you so much for those who reviewed and added to their favorites! It's very much appreciated!  
Disclaimer: All characters (except mine) belong to Wachowski's. You get it. Don't sue me...

They've been there for over a half hour. Now on the ground in each others arms, Neo spoke.

"We should get back to Lily."

Trinity didn't say anything; she only nodded against his chest. She got up first, held a hand out to Neo, which he took, and started down the deserted hallways. The elevator ride to their floor was slow and silent. Trinity's arms were wrapped around Neo's waist. He had one arm around her shoulders and kept a carefully composed expression.

It was Trinity who knocked on Link and Zee's door. Link answered it, yawning as he did.  
"We thought you'd never come!" he joked. They kept the same expression, brooding and devastated.

"What's going on?"

Ignoring Link's question, Trinity asked, "Where's Lily?"

"In our bedroom. C'mon."

Link led the way into his room to a laughing Zee and Lily playing 'Peek-a-boo' and singing nursery rhymes.

Trinity walked over to where her daughter was, smiling as Lily laughed at the game she was playing. Zee lifted the baby off her lap and handed her over to Trinity.

"Hey, sweetie," she whispered and starting playing with her as she talked with Zee.

"Link," Neo started, pulling him aside. "I need to ask you a favor."

"If you're gonna ask me to watch over your kid again, Neo, I swear to God-"

"Please." He begged.

"Fine." Link mumbled. "Neo?"

"Yes?"

"What happened?"

He sighed. "Umm… Trin and Lily can't be on the Neb anymore."

"What?! How the hell did this happen?"

"Link, I'll explain everything tomorrow."

"Yeah, okay. But you owe us for this." He nodded towards the others in the next room.

"I know."

"Trin," Neo said.

She was still holding Lily. "Yeah?"

Neo didn't say anything, but Trinity understood; they were going to leave.

She nodded. "Bye Zee."

Zee waved, "See you guys later." She muttered what sounded like "This will be fun…" under her breath but Trinity couldn't tell.

Trinity gave the baby over to Link. "Thank you," she whispered.

They left the apartment quickly. "Neo, what are we doing? Zee and Link are pissed!"

He chuckled, remembering Zee's twisted face when she realized what was going on. "I know they are." He took her hands into his, closing the gap between them. "But I need to be with you tonight. And tomorrow we'll spend all day with everyone else."

They both knew what the next day would bring them; a separated couple, very hard goodbyes, and what Morpheus would probably hate the most: 3 people aboard the Neb.

Trinity reached up to Neo's face. She put her hands on his waist and gently planted a kiss on his lips. "Then let's go," she whispered, breaking the kiss.

As soon as they were both in their apartment and the door was shut, Neo pushed her against the wall. Trinity's arms were wrapped around his neck. They kissed softly but rough; tender yet hard. Her legs were wrapped around his waist now –being held up by the wall behind them and Neo's strength. He pressed her harder into the wall, making her gasp, surprised. Trinity's hands were now caressing his back; his skin soft under the scratchy material of his shirt.

She got her feet back onto the ground. While being showered with kisses, she raised his shirt off, their mouths separating for only a second. She brushed her hands over Neo's now bare chest and back. Their mouths met again, pressing harder against each other. Neo's fingers were entwined with Trinity's hair.

Lips still together, Neo slowly slid her shirt off slowly, tracing with his fingers the familiar lines of where her ribs showed prominently from her skin.

Slowly backing away from the wall, they moved over to the bed together; still kissing each others lips, neck, and collarbone. Almost simultaneous they unbuttoned each other's trousers and both stepped out of them as they positioned themselves on the bed. Neo, on top, slowly kissed down his lover's chest, skipping over the thin piece of fabric connecting the sides of her bra together. Unfastening the hook in the front, he removed her bra and threw it into the small pile of clothes on the floor.

Both of them took of each others underwear, only bare skin touching now.

"I love you." Trinity moaned, while Neo kissed a certain spot behind her ear and squeezed the sides of her stomach.  
Throughout the night, the couple continued to make love, never letting go.

Holy… Snap. I'm sorry if you think it's bad. I promise to make the next chapter better. Reviews are definitely welcomed along with some constructive criticism!


	4. Chapter 4

Heyyyazz! (I don't know what that's supposed to mean…) I'm trying to be optimistic today but really, how can I? February vacation is over! Now I'll have a whole month and a half of school. So I meant to write some more but unfortunately I didn't feel like it.

Disclaimer: I don't own anything except my imagination here. So don't sue me.

Yeah, now to the story!

"Neo, we have to go," Trinity said in between kisses.

"We have time," he whispered. They were still in bed, their bare skin tangled in the sheets.

Trinity laughed. "Yeah, like 20 minutes." She looked over at the clock to make sure she was correct. "Sorry, make that 15 minutes."

Neo didn't care at all. Who cares if they're late? Well everyone did, actually… but whatever. He kept kissing her neck and as much as she enjoyed it, she had to protest.

"Please, Neo, we still have to take showers, get ready, and pack." Her voice almost broke on the last word. Neo pulled away from her neck.

He sighed. "Fine. I'll pack my stuff, you take a shower."

"All right," she smiled and kissed his cheek as she got up to get her clothes.

--

As soon as they knocked on the door, Link opened it.

"I hate you guys," he said, pointing an accusing finger at them.

"Good to see you too, Link," Neo said sarcastically. Trinity smiled.

"What happened?" Trinity asked.

"Lily! She would not stop crying! Now Zee's ticked off and I'm not in a good mood myself."

"Oh please, Link. You can have sex tonight," Trinity murmured.

"Yeah and you two couldn't have?" Link hissed.

Ignoring his comment, Trinity and Neo both led themselves into the room where their child began to cry – again, apparently.

Neo picked her up and hushed her. "Hey, it's okay. We're here… shh, shh…"

"Oh sure, it works with you," Zee mumbled as she walked out of the kitchen.

Neo chuckled. Of course he could quiet down his own child.

"Okay. Niobe, Morpheus, Ghost, and all them will be here in a like 10 minutes," Link told them.

"Wait who's 'all them'?" Trinity asked.

"You know, Sparks, Cas, Kid, Lock…"

"Link, are you kidding me?" Neo nearly shouted.

"Hey, they aren't _that_ bad!" He defended himself. Link looked to Zee for help but she seemed to have agreed with Neo and Trinity that some of their guests were not wanted.

"Uh, Link… you've met Sparks, haven't you?" Trinity asked. It was a rhetorical question, he knew. "He _will_ bring alcohol and I'd rather not have anyone here drunk today. Plus, Kid is only 17 and Lily isn't even 2 yet."

"Trinity if he brings any alcohol over just tell him he can't drink it here."

"Fine. But just be aware that Niobe will hate you too."

"Why?" Link asked.

"Because she and Lock used to be together. And she left him for Morpheus. Seriously Link, are you forgetting everything today?" Trinity said, half teasingly.

He thought for a moment. "No… but I thought Niobe and Lock were cool now."

She shook her head and mouthed a no.

--

Three light knocks indicated that someone was waiting outside. Link answered to door to his apartment to be greeting by a smiling Morpheus and Niobe.

"Hey, guys!" Link laughed.

He kept the door open to an already drinking Sparks and Ghost coming down the hall.

As soon as Ghost walked in, he saw Trinity's face and his brightened. She was the reason he kept fighting the war. Although he knew she would never love him in more than a brotherly way, he only hoped things could change.

Neo could see the delighted expression plastered upon Ghost's face. He was aware that he loved Trinity but he never said anything about it. If he ever did say anything about Ghost's love for Trinity, he was sure it would just make things more awkward for himself and Ghost and he didn't want to do that.

Trinity smiled up at her friend before he sat down next to her.

"Hey Ghost," she said, not looking at him but at her daughter sitting on her lap.

"Hi Trin…" Ghost almost whispered. He was still a little jealous of Lily. _She has the most amazing mother,_ he thought. It was true. Trinity was a very unique woman. He'd be the luckiest man alive (besides Neo) to have just a fraction of Trinity's beauty in his own woman. Maybe that was why he couldn't get over her - because he might never be able to find another woman like her in his existence.

He watched Trinity frown and followed her gaze to see Sparks taking yet another gulp of alcohol from the flask he kept in his pocket.

"Guys! Lock is coming and he's pissed!!" Kid shouted as soon as he ran into the room, letting himself into the house.

Niobe sighed and rolled her eyes. "Great," she muttered.

"What happened?" Neo asked.

"Well he knows that the Logos switched docking times with the Hammer. Listen, Niobe he's gonna-" Kid was interrupted by a furious Lock stomping into the room.

"Niobe! What the hell are you doing here?! I was just told by one of my men that you and the Hammer switched docking times! I came down here because I didn't believe it was true but since you are here I guess it is!" Lock's face was a bright red, one most of them were familiar with.

"Calm down, Jason." Niobe said.

"How can I calm down? You've disobeyed my orders far too many times! Maybe now you'll end up like Trinity here, stuck in Zion!"

"Hey!" Trinity defended. "It's not my fault…" she mumbled. Neo patted her knee three times in almost a joking sympathy.

"Jason, I really don't think that you would do that."

Still fuming he asked, "Why, Niobe, do you have to be so difficult?"

"Commander," Morpheus started. "I think it would be best if you were to leave now…" He said this calmly, hoping Lock wouldn't start anything against him.

Lock growled and pointed at Morpheus before storming out of the living room. If it weren't for Cas, who just walked up to the door, Niobe was sure he would've slammed it shut. Instead he just stopped short and stamped away, yelling nonsense down the hall. By now, Neo half expected Lily to start crying at Lock's yelling. For the daughter of a fearless fighter and the One, Lily was sure one to get upset easily. Her courage must be building up, he thought, smiling.

"What was _that_ about?" Cas asked about Lock's furious outburst as she brought her two children into the room.

"Aw, it was nothing. Just Lock bitchin' to Niobe again." A drunken Sparks said.

Cas scowled and glared at him.

"Sparks," Ghost got up and walked over to him and putting his arm around Spark's shoulders. "I think you're an alcoholic." He teased. He led him out of the room to take him into the second bedroom to have a behavior chat as if he were a child.

"Lily, look who's here." Trinity whispered into her ear. Lily then saw the other kids in the room and laughed, happy to see them again. Cas, being the only person close to Trinity who also had children, often set up play-dates whenever they were in Zion. One good thing was that there wasn't too much of an age difference between the kids.

Cas's daughter, Aliyah, was only four and her son, Hayden, was almost six. Besides, Aliyah loved to play with Lily. Cas had once told Trinity that Aliyah said she wished Lily was her little sister. They would probably like it a lot better now that they'd be in Zion permanently.

Trinity got up with Lily and sat down with her on the floor where Cas's children where getting many toys from their bag.

After a couple more hours of playing, eating, and socializing, everyone was getting ready to leave.

"We're leaving at 0500, don't forget." He reminded Link and Neo.

Neo felt a pang in his stomach. This would be the first time away from Trinity for more than a couple days.

"Come on Neo, let's go home." Trinity whispered.

"Yeah. Let's go home," he repeated.

Ahh, chapter 4 is finished! A MILLION thanks to those who reviewed! For you guys, I made this chapter a bit longer than the last one (eh, 900 words... I was cheap).

12/13/08 EDIT: I changed the spelling of 'Ahleah' from Ahleah to Aaliyah to Aliyah. All pronounced the same way, but I liked the newest spelling best. Strange fact: Aaliyah was the name of a singer/actress who died in 2001. She was supposed to play Zee in Reloaded and Revolutions.


	5. Chapter 5

Yo… So as I was rereading chapter 4 so that I could have it fresh in my mind, I realized I kind of portrayed Sparks as an alcoholic and Ghost as a jealous ass… but I really do like them both. That's why I loved ETM so much! Yeah, I know everyone's a little bit out of character (especially Trinity) but whatever.

And sooo many thanks to those who reviewed! You guys absolutely made my day!

Okay, so Chapter 5!! Whoo! (Oh yeah, you'll see in the story I made up a character, Jayne, who'll now be on the Neb with everyone… name based off Jayne from Firefly but their character personalities won't be anything alike)

* * *

The three slowly walked down the long corridors, making their way to the docking station. Trinity and Neo walked, hand in hand, and Neo carried Lily plus his bag. When they approached the Neb, they could already see six figures together: Morpheus, Niobe, Link, Zee, Kid, and Jayne.

"God damn," Neo said, his voice coated in misery, as he realized who the unfamiliar figures were.

When they were only several feet away from the rest of the scattered group, they stopped.

"Neo, Trinity," Morpheus nodded. Forgetting, he quickly added "Lily" and nodded again.

"Hey, Neo!" Kid ran up to him, excitingly. If it weren't for the state of depression he was in and lack of sleep he got, Neo probably would've punched the boy right in the face. "How's it goin'?"

"How do you think, Kid?" Neo asked sarcastically. Apparently he was in a very bad mood, too. Kid ignored his reply and went along anyways. "I'm so glad we'll be working together, Neo."

"Neo, Kid…" Morpheus gestured for them to come aboard. Niobe and Zee already said their goodbyes and were now leaning against one of the railing, waiting for the Nebuchadnezzar's departure.

Neo lowered his bag to the ground, taking one step closer to Trinity.

"Trin…"

"Neo, wait. I can't do this again. I'm not going to break down like earlier. I'm just going to tell you to be careful and that I love you." Her eyes were teary and bloodshot from the crying she'd done earlier.

"I love you too, Trin, "Neo whispered. He noticed Lily staring at him. Her dark blue eyes were looking between him and her mother and her mouth was dropped open. "And I love you too, Lily."

His daughter smiled and giggled. "But Daddy's going to go." She stopped laughing. Trinity pressed her hand to her mouth to keep a sob from being heard. It broke his heart to leave Lily here. "He has to, Lil'. But he's coming back - don't you worry. Bye Lily." He gently smiled and touched his daughter's cheek. Looking over at Trinity, he smiled again longingly. "Bye Trin." He gave her Lily, turned, picked up his bag and started walking towards the ship.

"Bye." A small voice said. Neo stopped and turned around. '_…That wasn't Trinity's voice…_' he thought. A grin spread across his face as he realized Lily had just said her actual first word. He almost ran back to a laughing Lily and smiling Trinity. "Oh, Lily," he laughed.

"Neo!" Jayne yelled from inside the ship. Neo looked back, nodding to Jayne.

"Good job, Lily!" he praised. "I love you two." He added and again, turned to get onto the ship.

"Bye!" Lily yelled. "Bye! Bye!" Neo laughed. He was proud of his daughter. He turned around, walking backwards onto the ship. "Bye!" he yelled back, waving his hand. The doors closed, making Neo's view of a laughing, waving Trinity and Lily into a rusty metal door.

He was still smiling when Jayne asked, "Is that your kid?"

"Yeah… her name's Lily."

Jayne smiled. "That's nice. I'm assuming that's your wife then."

'_Jayne obviously isn't a follower of the One; thank God_,' he thought. He and Jayne didn't know each other well. He'd seen him a couple times at temple gathering and meetings and such, but never talked to him. Trinity didn't know him either as he had just been unplugged a few months ago. "Wife? No. We aren't married, but we practically consider ourselves to be."

"Oh. Well its good you have people you're close to." He smiled again.

"Yeah, it is. I'll see you soon." Neo left to go put his bag in his room.

He put his clothes away, feeling weird that Trinity wasn't there with him. He sighed and plopped onto the bed. He laid there for a moment before deciding to go check the matrix code while they took off.

--

"Trinity, are you all right?" Niobe asked. They were still at the docks. The Neb was now far out of vision.

"Yeah, I'm fine. I just hope the oracle contacts them soon."

"Yeah, I get what you mean," Zee added. Trinity, Lily, Niobe, and Zee were all going back to Zee's apartment until the Logos would take off just a couple hours later.

Niobe laughed aloud, making all heads turn to her.  
"I was just thinking how long it'll be before someone decided to kill Kid and who it'll be."

Trinity and Zee laughed too. "I'm betting two weeks on Neo," Trinity said.

Everyone agreed. It wasn't that they hated Kid. It was just that he was annoying. Nobody really liked him when he was around, but they liked him when he wasn't. His incessant chattering reminded Trinity of Mouse; except she liked Mouse a lot better.

They entered Zee's apartment and talked for the next hour.

Trinity decided that before the Logos took off, she'd visit an old friend of hers.

--  
The door creaked open half way to reveal a friendly face. Once he knew who was standing before him, he opened it all the way and stood up straight.

"Hello brother," Trinity greeted. She'd known Ghost from the day she was unplugged. And he could say the same as they were freed on the same day.

"Trinity- what… are you doing here?" He asked while he gestured her to come in. "And where's Lily."

"Oh, Lily's down at the day care. I guess that's a good thing about being stuck in Zion. I got bored. And I wanted to visit you before you left."

"Oh. So how're you taking all this?" He asked gently, sitting down on a small couch next to Trinity.

Trinity sighed heavily. "I'm dealing. I probably feel worse about leaving Neo than he does leaving me."

"Why is that?"

"Because I have Lily. He doesn't."

Ghost nodded. "Yeah, that's true. I'm sure they'll be back soon… unless they're watching someone."

"Shit!" Trinity almost yelled.

"What?"

"We _are_ unplugging someone! Ugh, I completely forgot!"

"Well who is it?"

"I don't know. A girl, 16…" She tried to think. Trinity usually wasn't the one to watch her much. She was the one who made sure there wasn't any unusual activity inside; such as repeating codes or agents going after someone who wasn't a potential. These both happened sometimes.

"No, Trinity, that's good! She's only 16; she won't be allowed to work on a ship!" Ghost assured her.

"I'm not sure. Morpheus kept us on the ship after we unplugged Neo for over a month we were scheduled to come back to Zion. But those were under different circumstances."

"Exactly! So don't worry, Trin. They'll be back shortly. And hey, who knows? Maybe the oracle will want to see Neo."

"Yeah, maybe. But I don't like when Neo sees the oracle. Every time he does something bad happens."

"Trinity," Ghost sighed. "Never in my life have I met someone who worries as much as you do."

Trinity laughed slightly.

"Mmm. But I don't know… I've always felt responsible for Neo. Probably because I was unplugged so much earlier than he was and after everything we'd been through together I've always had the need to take care of him."

"You know he's the One, right?" Ghost joked. Trinity didn't like his rhetorical question. She didn't like them about Neo anyways…

"Shut up, Ghost." She joked.

He laughed again. "Okay, Trinity, you have to go. But I promise you, Neo, Morpheus, Link, and all them will be fine!"

"Wait, why do I have to go?"

"Because I have to go."

"Not for another hour!"

"Please, you know me. I pack at the last minute!"

Trinity smiled. "See you, Ghost."

"Yup, I'll try to swing by once more before we take off."

"Okay. Bye."

--

Just before knocking the door the Cas's apartment, Niobe rushed out almost slamming it into Trinity and Lily's faces.

"Oh!" Niobe yelled. "Trinity, Lily, sorry, I didn't see you!"

"Sure, it's fine. Wait, I thought you guys took off half an hour ago."

"We were supposed to. But I was running late and Sparks is complaining about a serious hangover he's got from drinking too much yesterday. So I don't know. Lock is going to be pissed when he finds out we didn't go yet!" Niobe was frantic, almost about to pull her hair out.

"Alright, calm down. I'm pretty sure Ghost is ready. I saw him less than an hour ago. And as for Sparks, just force him to get up! Okay? Niobe, it's his job."

"Okay, okay. You're right. So come with me."

"Wait, what?" For a moment Trinity thought she meant to come on the Logos with her.

"Just help me get Sparks and Ghost."

Trinity frowned a bit. "Sure."

"Sparks, get up!" Trinity shouted into his face. He was lying on the kitchen floor drinking again.

"But I still got to finish this bottle." He mumbled.

Trinity pried the half empty bottle from his hands. "No. You have to leave Zion." She looked over to Niobe. "Go pack his stuff for him."

"You're pretty…" Sparks slurred.

"Yeah, I know." Trinity muttered. She meant to be joking, but her tone wasn't convincing.

After about 45 minutes of packing Sparks's things and getting him off the floor and out the room, Trinity and Niobe had finally gotten everyone aboard the Logos.

"Trinity, thank you so much! I've been so stressed out with all this stuff going on with Lock and Morpheus… I guess you do too, but thank you!"

"Sure. It's fine, Niobe. Be careful out there."

"Yes, we will. See you soon."

The Logos took off, probably being piloted by Ghost, as Niobe had just left her a second ago and Sparks was drunk.

Now Trinity was alone. Of course, she still had Lily, Zee, and Cas. But she would miss everyone else. She was helpless now and there was nothing she could do about it.


	6. Chapter 6

Oh, Chapter 6. How I didn't want to write you and how every minute I would switch over to iTunes just to avoid you… Good times. Oh yeah, Jayne is a man (like the character from Firefly, if any of you have ever seen it…) sorry for any confusion there. The name Jayne pronounced like the girl's name (Jane) and Rae pronounced like the nickname for Raymond (Ray).

Reviews would be swell. :)

* (Edited January 28, 2009) 

"_All I ever wanted/ All I ever needed is here/ In my arms/ Words are very unnecessary/ They can only do harm."_ –Enjoy The Silence

"Trinity, seriously, you have to get up," Zee told her. "It's been over a week since Neo left!"  
Trinity lay still in her bed. She's probably only gotten up 5 times in the past week. She hasn't eaten much, showered, even talked since the Neb left Zion.

"Trinity, don't forget you have a baby to look after. And as much as I love Lily, I won't become her new mother," Cas said in a strict voice.  
Trinity bolted up at the sound of her daughter's name. "What time is it? What day is it?"

"Eleven thirty… on Tuesday," Cas said.

"Shit. Shit, shit!" Trinity yelled.

"Trinity, it's okay," Zee assured her.

"No. Oh, I'm such a bad mother. Ugh, what the hell am I doing? It's like Lily doesn't have a mom or dad right now!" Trinity was hysterical.

"No you aren't, Trinity. You're just going through a hard time. Besides, Lily is fine! She's at day care right now with Aliyah and Hayden." Cas said.

"Do you think she'll be mad?" Trinity asked.

"Of course she won't be mad. You're her mother," Cas said.

"I should go pick her up," Trinity thought aloud.

"Yeah, we'll do that in a little while… but first, you have to shower. You're starting to smell," Zee said. Trinity scowled.

"Okay, we'll come back in about an hour." Cas agreed.

"See you then!" Zee said.

A little less than an hour later, Zee and Cas came back to Trinity's apartment.

"Wow. You look a lot better," Zee said, staring at a very different looking Trinity.

Being freshly washed, her skin glowed, brightening her eyes a beautiful shade of blue. She put her shoulder-length hair into a half pony tail with a few strands of shorter hair hanging down on the side of her face. She was dressed in a khaki colored skirt and a sky blue, three quarters sleeve shirt accompanied by a pair of sandals on her feet.

"Yeah, well I'll be in Zion for a while. This is the most casual thing I have to wear around the city." Trinity said.

"It's a little dressy. We'll just have to go find you some new outfits," said Cas.

Before getting Lily, Hayden, and Aliyah, the three women went out clothes shopping, which Trinity strongly disliked. She wasn't the type of person to care about what matched or what looked good on her. In fact, the last time Trinity had gone shopping, she was with Switch, and it was months before Neo was even noticed in the Matrix. But that didn't matter now. Switch was long gone from Trinity's life and Neo was far away in the ruins of Earth somewhere.

The crew of the Nebuchadnezzar ate in the mess hall like they did every morning.

Link, chatting away as usual, spoke of a new recruit. "Who is she?" Kid asked.

"Just a girl who knows something is wrong about her world. Nothing special about her," Link responded.

"When are we unplugging her?" Jayne asked.

Link shrugged, looking up to Morpheus for an answer.

"Neo, when do you think we should unplug her?" Morpheus asked him.

After a minute of silence, everyone continued to eat their food, pretending that conversation never happened. Neo hadn't talked in days. Link one day, got so tired of asking yes or no questions that Neo could nod to, he yelled at him saying that they would actually leave him in the middle of nowhere if he didn't stop giving them the silent treatment. Of course, Neo didn't respond to Link so he just locked himself in his room for a day and a half. After that, nobody decided to threaten Neo or aggravate him.

"Is she ready?" Neo finally asked, breaking the silence with a scratchy voice he hadn't used since days ago.

Jayne snapped his head up; he hadn't heard Neo's voice since their talk about Lily and Trinity while leaving Zion. Link's jaw was dropped open, amazed that he finally spoke.

"Yes, I do think she is," Morpheus said.

"Then as soon as possible," Neo said, getting up to rinse out the bowl of goop he didn't eat.

"Alright. So we'll go in later today if we can." Link said. Morpheus nodded to confirm Link's plan.

Neo left, heading to the Core to watch the Matrix. They would be going into the Matrix in a few hours and he had refused to jack in since Trinity left. The last few days he had been really useless, he realized.

A couple hours later, Link came down to the core to find Neo still watching the coding of the Matrix. "We're going in now, Neo," he said.

Neo nodded. Link wasn't sure if he was reverting back to his familiar quietness or if he was merely at a loss for words. "So are you back to the silent treatment, or what?"

"No. I just didn't have anything to say to you." Neo mumbled.

"Oh. That's good then. I know how you feel, Neo. We all do. I have to leave Zee all the time and Morpheus has to leave Niobe…" Link trailed off, focused on the code of the Matrix. Neo didn't respond as he too was busy watching the Matrix. They both watched the screen intently as Morpheus came down.

"What is it?" he asked.

"Agents," Neo whispered. "They're after the girl."

"Shit," Link muttered, setting up their entrance into the matrix.

"Neo, jack in now! We'll follow you in," Morpheus said, running over to the chair Neo was always plugged into.

Neo took a moment to pinpoint the girl's location then ran to Morpheus, not preparing himself for the slight pain whenever he was jacked in.

"Jayne, Kid! Get down here!" Morpheus shouted. Less than a minute later, the two boys arrived, and in another minute, they were all jacked in.

Neo reached the girl before the others. Flying through a crowded city, trying to find a way to get the girl without getting her killed. She was running down a lonely street, three agents after her. Her upper arm and side was bleeding. As she rounded a corner, Neo flew down, surprising the agents he now faced. Neo moved swiftly to avoid all shots and attacks the agents tried to throw at him. Neo snapped one agent's neck, all while shooting one through the head. The last agent, terrified, backed himself into a corner before Neo rearranged his code to make him immobile. He shot the agent three times, just to be sure. A block away, Neo heard screaming.

"Shit," he muttered. Someone heard the gunshots.

He ran to find the girl. It wasn't hard; she was lying on the ground, propped up against the fence and the wall, blocking her from running any further. She was holding her bleeding arm, crying.

"Get up." Neo said harshly. He didn't mean for him to sound like another bad guy, but apparently he did.

"Who are you? What the hell do you want?" She cried.

Neo crouched down next to her.

"It's okay. I'm here to help you." He said gently. "Let me see." He lifted his hand to move hers away from her wounded arm. Arranging her code, he pushed the bullet out of her body and forced her skin together, healing the wound. Doing the same to her grazed hip, she looked at him wide-eyed.

"How… did you do that?" she asked.

Neo slightly laughed. "Come on. We have to go." He pulled her up and took her forearm to make her follow him out of the alley.

"Wait!" She protested, digging her black and white Adidas shoes against the cement ground to make Neo stop pulling her. Neo let go of her arm.

"What?" he asked.

"Who are you?"

"My name is Neo."

"Oh. My name's Rae."

"I know." Neo said, taking her arm again, running with her down the street. Police cars were passing them, oblivious to them running down the sidewalk or else they would have had some serious trouble with them. Crowds were forming behind them, trying to see the bodies returned to their original form.

Reaching the old apartment, Morpheus, Jayne, and Kid were already there.

She looked horrified. God, she must have thought we were in some huge gang or something. Neo wouldn't be surprised if Rae actually did think that. The four men did look a bit frightening; Neo in a black trench coat, Morpheus in a black suit, Jayne wearing black jeans and a leather jacket. Kid took the time earlier to customize his outfit. He wore a pair of Doc Martin's and a Misfits t-shirt. Neo wondered if that was his usual attire in the matrix.

Morpheus made his speech about reality and when given the choice, Rae took the red pill. Jayne led her into the other room, sitting her down in a chair. Her legs were shaking when she sat down a she felt very uncomfortable.

Rae looked abnormally skinny in her straight legged jeans and baggy softball shirt. . She had long reddish blonde hair let down, reaching her elbows; too bad the next time she woke up, it would be gone.

She looked over to Neo, who smiled back at her. Next, she turned, looking into a cracked mirror, ignoring the man who put strange pads on her pulses. She leaned forward, looking at her ruffled hair and pink face. Her whole body was uncontrollably shaking now.

Watching her reflection in the mirror, the glass started to move, healing itself, distorting her face until it was clear again.

"W-what did y-you d-d-do?" She stuttered. This wasn't real. She must've been dreaming. Wake up, she told herself.

She stupidly touched the mirror. It stuck to her. It stuck to her? Now she was positive she was dreaming. The mirror started to spread up her body.

"Link, are you ready?" Neo asked into his cell phone. "Good. Get us an exit too."

He hung up.

"Ready for what?" She choked out. The mirror was still going over her skin. She started to scream until the substance swallowed her completely.

Neo unplugged Jayne, and then the two men went over to the infirmary where an unconscious Rae was.

"Is she okay?" Jayne asked.

"She's fine," Link responded.

"Where am I?" Rae asked groggily.

"You're in the real world now. Don't worry, we'll explain soon. Just get some rest." Morpheus said.

Rae barely nodded and followed his command.

"She'll be up in a few days. She's young so she won't need much work," Link told the crew.

"I suggest the rest of you find something to do while we get her adjusted here," Morpheus advised.

Kid, Jayne, and Neo nodded and went off to their cabins.


	7. Chapter 7

Oh, I'm in a good mood. I've got my Monster energy drink, my music, and written chapter. :)

"There's one thing I want to say, so I'll be brave/ You were what I wanted/ I gave what I gave/ I'm not sorry I met you/ I'm not sorry it's over/ I'm not sorry there's nothing to save."

*(Edited January 28, 2009)

Chapter 7

---

It was dark- that was for sure. Her eyes closed but she could see everything happening.

She cried, but not for the pain she was in, but because she knew she would never see her daughter again; or Morpheus, Link, hell even Kid!

"Trin?" a whisper ahead of her asked.

"Trinity?" the voice said in almost warning her to answer or else something would happen.

She tried to speak, but the words wouldn't come out. "Trinity!" the voice yelled again.

Finally she remembered all that had happened: she and Neo made it to the machine city, just like he said they would.

"I'm here," She finally choked out.

Finding his way to her, she could already feel herself fading away.

What seemed like a second later, Trinity saw Neo die. "No!" she shouted. He couldn't have died! Not at the hands of Smith. Trinity watched in horror. She knew she was dead, but somehow she saw it happen as if she were standing right next to the men. Neo was copied into a Smith just like all the others. _This isn't real_, she told herself.

"Neo!" she screamed at the top of her lungs.

She bolted up, now sitting at a 90 degree angle in her bed. As a reaction to her scream, Lily did the same. Trinity was crying, tears staining her cheeks, gasping for breath, before falling onto the bed for a moment, wet with sweat and tears. She rolled off the bed before going into the next room to care for her daughter.

Picking her up from the crib, which she was already standing in, Trinity hushed her, walking with her into the kitchen. Checking the clock, Trinity groaned. It was already four thirty in the morning. There was no point going back to bed now as Zee said she'd come by before six to help Trinity find a job. She didn't know how much longer she'd be on unpaid leave from the Nebuchadnezzar, so she figured a job could only do her good.

Lily had learned four new words in the past week: Mama, hi, no, and her favorite word: bye. She was still working on the word 'Daddy' but couldn't quite say it. It'd also probably help if her father was with her too.

Setting Lily down in a high-chair, Trinity walked to the pantry in the dimly lit kitchen. Finding nothing but mushy carrots in a baby food jar in the pantry, Trinity cursed under her breath. She took the container and opened a drawer to get a spoon. Bringing the food back to her daughter, she muttered, "Sorry, Lily, but it's all we have."

She opened the lid, the smell of carrots contaminating the surrounding air, making Trinity wrinkle her nose. Taking a spoonful to Lily's mouth, she turned she head, refusing to eat it.

"Lily." Trinity admonished. Trying again, Lily still refused.

Trinity sighed in frustration, getting up to lean against the back of the chair. Lily stared at her for a long time. Looking up to meet her stare, Trinity asked quietly, "You aren't going to behave for me, are you?"

Lily still stared until finally smiling with her tiny teeth.

Trinity smiled, hopelessly, kissing the top of her daughter's head and smoothing out her hair. She looked at Lily's eyes again before saying, "You're just like your father."

Trinity made Lily a bottle, telling her this was the last time she would ever have one. After she finished her bottle, Trinity put Lily back in her crib, letting her sleep for another hour before Zee came. Trinity took a shower, put on some clean clothes she had recently gotten, and laid down on the couch. Exhausted, but not daring to fall asleep in fear of her dream, Trinity watched the clock and waited for Zee.

Thankfully for Trinity, Zee arrived early. She'd brought over a coffee for Trinity and they talked about a good job she could start.

"Well what are you good at?" Zee asked.

"Umm," Trinity thought for a minute. "Fixing things on ships… fighting… again, I'll say fighting… and poker."

Zee stared at her in disbelief. "So, we don't have many options."

Trinity agreed.

"Yeah, I'm going to tell you to either be a mechanic or a personal trainer. Both jobs suck but at least you'll make some money. Or you could just gamble the money you have, but I wouldn't suggest it."

"Uh huh. I'll have to think about it…" Trinity said.

Zee nodded.

"Oh, I have to go food shopping. Do you want to come?" Trinity asked.

"Sure. What do you have to get?" Zee asked.

Trinity laughed. "Everything," She replied.

Zee showed Trinity to the closest market that sold everything she needed.

Fortunately, it wasn't crowded. At approximately six fifteen on a Saturday morning, not many Zionites were awake.

Zee helped Trinity by picking out ripe fruit while Trinity and Lily browsed the stands.

Trinity saw several racks filled with appropriate food for Lily. Looking for something that appeared to be somewhat tasty, Trinity's name was called by a man.

She pivoted on the ball of her foot and her heel so see a smiling elder man coming towards them.

"Hello Trinity. Hello Lily." He said.

"Councilor Hamann." Trinity nodded, moving her eyes back to the shelves.

The Councilor looked at his feet, only about three steps away from her.

"Trinity," he started "I have known you for a very long time."

"Yeah, what are you getting at?" she asked coldly.

"I only mean to say that I hope there are not any negative emotions between us."

"Councilor, I've been on the Nebuchadnezzar for over 7 years now. You separated me from my home. You took Neo away from me and his daughter! Can you really expect me to not have any 'negative emotion'?" Trinity hissed.

"I voted against this, Trinity. I know that you would much rather be on that ship with Neo."

"You _voted_ on this?" Trinity asked skeptically. "Did the council think about how your idiotic decision could affect the outcome of this war?"

Councilor Hamann remained silent, making Trinity assume the answer to her question was 'no'.

"That's what I thought. So please, councilor, don't disturb my family any more than you already did." Trinity spat, brushing past him to get Zee.

"Trinity, wait." The Councilor said. "I know you're not being paid, so I could get you a good job for you to take on while you are not serving aboard a ship."

"Really? _You_ would do that?" Trinity asked, her voice still angry.

"Yes. If it would help mend our friendship I could."

"I'm sure the council wouldn't appreciate it."

"Please, Trinity," the Councilor said.

There wasn't much of a friendship anyways but Trinity took his offer. "Fine. I'll take it," she said, calming her voice.

"And you will promise not to be angry?" Councilor Hamann asked.

"Yes," Trinity said.

"Good. Then I will visit you later and make sure I have a fitting job for you."

---  
"So how long do I have to eat this stuff?" Rae asked, disgusted by the chunky goop in front of her.

The whole crew was sitting with her in the mess hall but nobody answered her.

"Okay…" she mumbled. Speaking up, she asked, "Umm, what do you guys do for fun around here?"

"Nothing," Link replied flatly.

"You're telling me that all we ever do around here is eat, sleep, fight, and fix crap?"

"Pretty much. Except Neo doesn't really qualify for the first two." Link said laughing until Neo glared at him.

Rae saw it and of course questioned. "Yeah, what's up with you? I don't think I've ever heard you say more than 5 words –that weren't swears- since I've been here. And seriously, has that spoon _ever_ touched your mouth? I mean you're probably going to die of starvation, for God's sake."

"Shut up, Rae," Neo said, recognizing his tone as Apoc's when Mouse was talking to him during one of his first days on the Neb. He smiled sadly, thinking of how positively different his life would've been if Cypher hadn't betrayed them.

"Aren't there ever any girls here I could talk to?" Rae wondered aloud. "You guys are just so dull!"

"Well there used to be but then she got taken off the Neb because-" Kid started to say, but then stopped.

"Because why?" Rae asked him.

"I'll tell you later," Kid whispered.

"You better not, Kid. If you do, I swear to God, I'll kill you." Neo threatened, partly exaggerating.

Kid stopped talking about Trinity and acted like he never responded to her question. "Anyone your age? No. You're too young to stay on the ship. That's why we're taking you back to Zion after we take you to the Oracle," Kid said.

Neo heard this, causing him to jump up from his seat on the bench across from the two teenagers. "What?" he almost yelled. "We're going to Zion?" he looked to Morpheus, who nodded a yes to Neo.

Neo cleaned his dish and ran to the Core, settling himself into the operator's chair with new hope boiling inside him.

Back in the mess hall Rae asked, "What was that about?"

Morpheus responded by saying, "Neo has a family back in Zion. They were taken off the ship just a few days before you were unplugged. Needless to say, he didn't take it well."

Rae didn't say anything back. Instead, she wondered about Neo's family and the reason why they were removed from the Neb. She figured she would just ask Kid about it later, despite Neo's threat.

Just over two and a half hours later, Neo got a call. It was from Niobe; she had called the Neb from inside the Matrix.

"Operator." Neo said.

"Neo, its Niobe. We got a message from the Oracle today. She needs to see you. Bring your new recruit with you. Apparently the Oracle needs her too."

Neo sighed, relieved. "Thank you, Niobe."

"Neo?"

"What?"

"Just make sure you do what she tells you. I want this god damn war to end." Niobe hung up before Neo could respond to her.  
"Me too," He said to himself. Remembering the purpose of the call, he yelled to Morpheus, telling him to come down to the core.

"Neo, what is it?" he asked when he saw Neo with a grin planted on his face. Jayne was with Morpheus too. He must have been teaching Jayne something.

Jayne almost gasped when he saw Neo actually smiling.

"Niobe just called from the Matrix. The Oracle made contact with them."

"What did she say?" Morpheus asked.

Neo wasn't sure if he meant Niobe or the Oracle so he guessed Niobe.

"Niobe said the Oracle wants to see Rae and me," Neo told him.

"Good. Then we're going in tomorrow. And unless the Oracle says otherwise, we're going back to Zion to drop Rae off and recharge."

"I can take my shift now." Jayne suggested, figuring Neo was probably tired now.

Neo nodded thankfully and walked to his room, feeling the happiest he had ever felt after the meeting with the council.

---  
Several hours later Councilor Hamann knocked on Trinity's door.

She smiled and invited him in.

"Trinity, I had a bit of trouble finding something for you but I think this is the best one I could get."

"What is it?" Trinity asked.

"A teacher."

"A teacher! Councilor, I don't know a single thing about teaching!" Trinity cried.

"That's alright. You will just be a substitute while the other one is in the medical ward. All the materials you need to teach will be provided and over half of it is about the Matrix. You'll be fine there," Councilor Hamann assured.

"Yeah, okay." Trinity said, accepting the folder about the teaching system that Councilor Hamann got.

"Oh, I just remembered. The Logos reported to us that the Oracle wanted contact with Neo and their new recruit, Rae. So who knows? Maybe you won't need that job after all."

Councilor Hamann left and Trinity shut the door. She smiled widely, thinking about how she and Lily would soon be placed back on the Nebuchadnezzar with Neo.


	8. Chapter 8

Thanks for the reviews everyone! I really appreciate them!

"_Some people have to be/ Permanently together/ Lovers devoted to/ Each other forever/ Now I've got things to do…"_

_

* * *

  
_

Morpheus was on duty watching the Matrix when Neo walked in, responding to his call.

"Neo, we're going into the Matrix soon. I suggest you get Rae in here and help her set up," Morpheus said.

Neo nodded and went to Rae's room, Neo's old one. He didn't bother knocking and entered the room to find Rae wasn't there.

Neo finally found her in the mess hall, laughing with Kid and Jayne. Rae greeted him in a high pitched voice, like she was a hyper eight-year-old.

"Um, hi. Rae, we're going in to see the Oracle. I've got to set you up…" Neo said awkwardly.

"Alright," Rae said as more of a question than a reply. She'd only been jacked in twice- once when she was first unplugged and learned what the Matrix was and when she started her training.

"Just come down to the core in a few minutes," Neo clarified.

"Do you need us?" Jayne asked.

"I don't know," Neo responded. "Come anyways."

When Rae, Jayne, and Kid finally entered the core, Morpheus explained their mission once again; to get Neo and Rae to the Oracle without getting anyone hurt and avoided agents the best they could. Neo didn't feel that this was a dangerous mission at all –if they did run into an agent, he could easily take him out– but Morpheus took every mission this seriously since Cypher's betrayal.

The five of them jacked in, Morpheus made the call to Link to let him know they made it in safely.

The sky was extremely dark for six o'clock, Matrix time, in the middle of summer. Neo didn't see anything wrong with the coding of their environment but he kept an eye out for anything unusual.

Instead of cramming into a car, they walked briskly in the abandoned streets of New York –another sign telling Neo something was wrong, as New York was never this lonely- heading towards the apartment buildings a few blocks away.

"What are you looking for?" Rae asked Neo, who was walking beside her.

"I don't know," Neo answered. He searched the code, over and over again. Something was going on - if only he could find out what.

After several minutes of unsuccessful 'code browsing', they were already at the Oracle's apartment, so Neo decided to ignore the strangeness of the matrixuntil after his talk with the Oracle.

Neo told Rae to go to her first, he needed time to think of what he'd say.

Rae walked awkwardly into the doorway. The Oracle was baking cookies, reminding Rae of her grandmother before she passed away.

"Rae, sweetheart, have a seat, please." The Oracle said.

Rae didn't like when people she didn't know called her 'sweetheart'. She sat in one of the wooden chairs at the glass table and put one leg on the edge of the chair, hugging her knee. While waiting for the Oracle, she traced the squares of her rip-stop camouflage pants. Rae started to get annoyed; this 'Oracle' was too busy baking cookies when an agent could come in and kill her at any second. She didn't trust the Matrix now that she knew the truth.

Finally the Oracle turned to face her. "Sorry about that, hon."

Rae gave her an aggravated glare; first, because she called her 'hon' and second, she still wouldn't tell Rae her 'destiny'. She was starting to think this whole meeting was just a waste of time and what the rest of the crew thought was a joke.

"So are you planning on telling me why I'm here anytime soon?" Rae asked.

The Oracle laughed. "You are here because you know about the Matrix and to hear what your part in the wars end is."

"Want to tell me?" Rae asked, still aggravated but giving her a chance now that she was about to answer her question.

"Mmm, you have a very important role. You do not know much about Neo's past, do you?" The Oracle asked. Rae shook her head and the Oracle continued. "Don't worry, you'll know sooner or later. The time will come where you will have the chance to help Neo. It will be an extremely important decision, whether you choose to help or not, so I suggest you should think through it many times."

At this point, Rae wasn't angry. Just confused. "What do I have to help him with?"

"A decision that may take the war to its end," the Oracle responded.

"Are you saying that I choose whether the war ends or not when I've only been out for less than two weeks?"

"I told you that you're important," the Oracle said, smirking. "I'm sorry Rae, but I can't tell you anything else. It'll all become clear when the time comes. If you could send Neo in for me, I must speak with him too."

Getting up slowly, Rae nodded, walking out the door to see Neo leaning against the wall farthest from the kitchen.

Neo watched Rae walk out with a puzzled expression pasted on her face. Her eyebrows were pushed together as she thought about what the Oracle just told her.

Neo moved off the wall, heading towards the entrance before Rae could tell him herself.

"Ah, Neo, I knew you'd have questions for me, as always, so that's why I told the Logos to send you also."

"You're right. But I have to ask you something more important right now."

"Shoot."

"What's wrong with the code? It isn't normal and I know you know why," Neo said.

"You know the answer yourself. I'll tell you though. It's Smith. As you know, he's been copying his code into other humans and programs, allowing him to take over his or her body," the Oracle said.

"It's worse than you thought." Neo said, reading her thoughts.

She hesitated. "Yes and unless you do something about it, it will only get worse."

"What can I do?" Neo asked.

"First, I'll tell you this: You need Trinity. Together you can end the war. I know getting her back will be a problem but I think that it is possible. Rae's a smart girl, she can do something."

"_Rae_?" Neo asked. He suddenly wished he listened to Rae's conversation with the Oracle to know just what she was talking about.

"Yes. Rae can help you if she wants. I believe she will but I honestly don't know."

"Why?"

"Because she hasn't made the choice yet. You know better than anyone Neo; nobody can see the future unless they've made a choice, not even me."

Neo had already knew that but asked anyways. He hoped Rae would make the right decision. He was almost positive she would, but there was always a chance…

"Neo, you won't like what you're about to hear. The council told you that once you had contact with me, they'd put Trinity and Lily back aboard your ship. Unfortunately, this will not be enough for them. The council is looking for answers of when the war will be over. You know just as I do that we cannot say."

"You said Trinity wouldn't be able to come back here unless I knew exactly when the war would end," Neo said. The Oracle nodded. "Does this mean that Trinity will never be able to be put back on the Neb?"

The Oracle nodded. "You'll just have to get her back another way."

"How?" Neo asked.

"I would tell you… but it'd be better if I didn't."

"What's that supposed to mean?" Neo snapped. He was getting angry with her today. She wouldn't tell him a single thing that could help him get Trinity and Lily back or how to stop Smith and the machines.

"Neo, I'm sorry, as much as I want to help you, I can't. You must get back to the real world," the Oracle suddenly said.

"Why?" Neo asked, now as anxious as she was.

"In a moment you'll see as I do and you won't want to deal with it…"

Neo scanned the code and as the Oracle said, he did see it. Hundreds of Smiths were close to them; only about a mile away.

"Thanks," Neo muttered before running out the door.

He grabbed Rae's arm, making her run with him just like the day he unplugged her from the matrix.

They left the apartment meeting Morpheus, Kid, and Jayne in the hallway. "We have to go, _now_," Neo said urgently.

Morpheus didn't question but only ran to catch up with Neo and Rae. On his cell phone, Neo called Link to get an exit.

"Take a right when you get out of the building, down six blocks into the old hospital. Go to the reception's desk, I'll be waiting."

"Nothing's closer?" Neo asked.

"Nope. Why? What's the hurry?" Link asked.

"That's the direction Smith coming in."

"Shit. Neo, by the time you get about four blocks there, you'll meet Smith. You've got to do something or you'll get all of us killed, Neo."

"Fuck. We'll make it, Link." Neo hung up his phone.

"What's wrong?" Rae asked him.

"Smith. He's close and we might not make it," Neo said, feeling no need to lie to her. They'd all get killed, he was almost positive they would.


	9. Chapter 9

"When do you think I'll be okay/ If I should stay when do I pray/ If I should stay where do I begin/ Do you think I should watch you die/ Should we close our eyes and say goodbye" -Miss Blue, Filter

-Sorry for any typos or mistakes... I didn't proof read. Reviews would be nice, if you can. =D  
Disclaimer: I don't own The Matrix

Chapter 9!

* * *

Over two blocks away from the Oracle's apartment building, Neo could already see hundreds of Smiths walking into view.

"Morpheus, get them to the exit. Take any path but don't stay on this street," Neo said.

Morpheus obeyed and took Jayne, Kid, and Rae into the nearest alley to lead them to the abandoned hospital.

Smith finally caught up to Neo, who was standing in the middle of the street.

"Mr. Anderson, good evening," Smith said. "I was hoping your new group of… _humans_… would be joining us today, but to hope is to dream. And, Mr. Anderson, you know as well as I do that _this_ is just a world full of dreams." He motioned to the buildings around them. "Dreams are pointless, as is hope."

"When's this going to end, Smith?" Neo asked.

"It will end whenever you want it to," he responded. "But you'll have to fight for it. And as of now, you are thinking of what the Oracle told you: you will need your human to help you end the war."

"How do you know that?" Neo wondered aloud.

"I know everything." Smith replied. "I know how you feel… what you're thinking… what you _want_."

Neo glared at him wondering if Smith was lying or not.

Morpheus, Jayne, and Kid reached the phone before realizing Rae wasn't with them.

"Where is she?" Jayne asked Link, over his cell phone.

Link searched for her in the Matrix before saying, "Oh, no. She's watching Neo and Smith."

"_What_? She'll get herself killed!" Jayne yelled into the phone.

"Yeah, I know, but if Neo knows she's with him, he'll make sure Rae doesn't get hurt," Link said.

"Does Neo know she's there?" Jayne asked.

"I don't know. Jack out, its dangerous here now with so many Smiths."

Jayne hung up and answered the ringing phone first then getting unplugged by Link.

Morpheus came out last, late because he retraced their steps looking for Rae without getting himself in danger.

"Call her, now," Morpheus demanded. He was angry now, thinking Rae should've known better.

Smith was still talking to Neo while Rae was pressed up against a brick wall, out of Neo and Smith's view. Her cell phone rang loudly; as she had forgotten to put it back on vibrate after fooling around with it in the Construct. The sound startled her, making her jump and reach for it quickly. As a result of her clumsiness, she dropped it to the cement, cringing at the sound of it hitting the ground. She now regretted staying behind to listen to Neo and Smith's conversation.

Neo heard the noises coming from the alley and moved slowly to see what was happening. Before Neo could move to it and Rae could pick up the phone or run, a Smith clone found her in the alley.

"Well, what do we have here?" Smith laughed at Rae, who was terrified when the Smith pulled out his gun. He raised it to her chest but before he could shoot her, Neo interjected, knocking the gun out of Smith's hand.

He pushed Rae down the alley, forcing her to run faster. The Smiths were running after them, trying to shoot Neo and Rae as they moved. A bullet grazed Neo's arm but he ignored it as if it never hit him.

Almost five feet away, Neo and Rae saw the hospital that was their exit.

Bullets were missing them by inches until one hit Rae in the center of her back.

She screamed out of pain and fell to the ground. Neo forced her to get up and he held up most of her weight, carrying her into the hospital.

The phone was ringing when they got in and Neo immediately put it up to Rae's ear. He hung it up again and answered it just as Smith tried to shoot him. Neo was too fast and made it out of the Matrix safely.

He was unplugged by Link, the only one who wasn't helping Rae get out of her chair without feeling the pain of the bullet she was shot with inside the Matrix.

Although she it was only her mind that was making it real in the Matrix, she could feel the pain physically in the real world.

She got up, wincing, and looked at Neo.

He stared back for a moment before leaving to go to his cabin where he would inspect his arm, probably bruising now.

Trinity got up extra early in the morning, so she could get ready for her first day of work. She dropped Lily off at daycare, which was now becoming a regular routine.

She sat on top of the desk in the large classroom, rereading the curriculum she would teach throughout the day.

Teenagers, around sixteen or seventeen years old, entered the classroom noisily, eyeing Trinity curiously. A loud bell rang, indicating that whoever came in the class by now was late.

Trinity hopped down from the desk standing in front of the class nervously.

"Um… hi," she started. "I'm Trinity; I'll be your substitute while your teacher is out…"

A boy raised his hand and spoke out, "Are you that chick that got kicked off a ship the other day?"

Trinity's face flushed. Apparently everyone knew about it now. She didn't answer the boy's question.

"I'm handing out a sheet that you will write your name on. Pass it around the class, write your name and give it back to me." She said, giving the paper to a girl sitting in the front corner.

Trinity saw another girl whispering to a boy sitting next to her and asked "Do you want to share with the class?"

The girl responded by saying, "Sure. I was telling him that you were kicked off your ship because you were a whore and slept with '_the_ _One_' then had his kid."

A few kids tried to suppress a laugh while others stared at Trinity. Trinity glared at the girl and decided to ignore the response.

When she finally got the paper back, Trinity frowned. Either the kids took her as a joke or they just wanted to be smart asses and aggravate her as the paper came back with two sheets filled with 'Your Name' printed on each line. Only one line, the last one, had a name written on it.

"Okay. So it seems that everyone except for 'Nat', who filled in her name, will be issued demerits today." Trinity said.

"What?!" One girl yelled out over the other children's complaints.

"Quiet!" Trinity yelled. "I don't like being strict but being a former second-in-command, I've learned to deal with it. Now you can either work your way to my good side, where I'm not a bitch, or you can stay on my bad side, where you don't want to be," Trinity said.

The kids in the class were quiet and obeyed Trinity's command to fill out their real name.

This time, Trinity smiled when she got the paper back although there were still a few kids who still put down 'Your name'.

"Good. I still have a couple kids in here that I can make miserable."

Trinity put the paper down on her desk and smiled wickedly at the faces of horrified students who decided to mess with her.


	10. Chapter 10

Ugh. I've got testing this week so don't be surprised if I don't update.  
I'm still not really sure I like last chapter but if it was read and got reviews, I'm fine with it, I guess  
Thank you so much everyone for the hits and reviews! You're so awesome! :D

"_What you want/ Is something you need /And what you've wanted /Is something I bleed/ Could you say to me you love me/ And I'm the only one" –I'm Not The Only One, Filter_

(Big moment for me) Chapter 10!

* * *

After a day of resting, Rae finally woke up to a growling stomach. Soon after she was shot and unplugged from the Matrix, she passed out on the way to her room.

Rae walked past Morpheus's cabin, still adjusting all her senses to the loud ship, when she heard her name. She pressed her ear up to the crack on the door and heard Neo talking.

"Rae had no right to do that, Morpheus! She almost got the two of us killed." Neo almost yelled. He sounded angry; Rae knew she should leave but was interested in what he had to say about her.

"Neo, calm down. I know you don't like what Rae did but she doesn't know any better. She's sixteen," Morpheus said.

"Morpheus, that's exactly my point; she's sixteen! I'm betting the council knows about her and they'll expect her in Zion soon," Neo said without much of a tone, taking his captain's advice and calming himself.

"Yes, we are going to Zion… eventually. I'm curious as to what the Oracle told Rae and how it would be helpful to us. Don't worry, Neo. I'll speak to Rae about her behavior and the council. They may let her stay aboard along with Trinity and Lily's return," Morpheus said.

"They can't come back yet," Neo said, quietly.

Morpheus was obviously confused so Neo explained further.

"The Oracle told me that when the council said they wanted me to meet with her then Trinity could come back, they really meant they wanted to know when the war would end. Smith said anytime I wanted it to, but I know it isn't that easy."

"Hmm. I understand. Then I suppose we'll have to find something else to say to the council." Morpheus said.

Rae didn't hear Neo say anything, so she assumed he only nodded to Morpheus.

A second later, Rae stumbled into the room when Neo opened the door. Regaining her balance, Rae started babbling an apology but Neo walked out of the room, ignoring Rae.

He was acting like a little kid, being mad at Rae, but he didn't care.

Neo walked into the mess hall, getting himself a bowl of food, when Rae ran in.

"Neo, I'm so sorry! I shouldn't have been listening to your conversation with Smith or Morpheus! Neo, please-" Rae started, almost crying, until Neo interrupted.

"Rae, its fine. I overreacted, I know," Neo confessed.

"I'm really-Wait… what?" Rae asked, confused.

"I overreacted. I shouldn't have gotten mad. I mean, it was your first time being plugged into the Matrix. I can only imagine how curious you are now, especially after talking to the Oracle," Neo said.

Rae couldn't help herself. She closed the gap between her and Neo, and stood on the tips of her toes to kiss him. At first she was nervous, wondering how Neo would react, but then when she felt him kissing her back, she stopped her worries. Neo pulled back just a little bit, allowing himself to say, "I'm almost twice your age, Rae."

"I don't care," she responded. Rae pulled Neo's neck back down to her face, kissing him again, until she pulled away because of the footsteps heard down the hall.

Neo left quickly, leaving Rae in the mess hall with Jayne, who just came down. He went to his cabin thinking about what just happened. _How can I ever tell Trinity about this?_ he thought. As much as he enjoyed his encounter with Rae, he couldn't imagine the thought of Trinity's reaction to this without getting sick.

* * *

Mwa ha ha! I'm evil, I know. Hope you liked this chapter. Update will probably be next week… sorry it's so short! I'll make it a lot longer next time.


	11. Chapter 11

Gahh! Chapter 10, you got no reviews. Yikes. Ah well, maybe this one will. Anyways, testing is done until May (yay!) so you'll see me around now.

Disclaimer: Me no own Matrix

"So impressed with all you do/ Tried so hard to be like you/ Flew too high and burnt the wing/ Lost my faith in everything" -Somewhat Damaged, Nine Inch Nails

* * *

"Did something just happen?" Jayne asked, seconds after Neo left the mess room. "Neo practically ran out of here."

Rae didn't respond, she only shook her head and laughed quietly.

Jayne got himself and Rae a bowl and sat down across from her.

After a few minutes of silence, Rae asked, "So, does Neo really have a family in Zion?"

"Yeah. He he's got his girl back there and a baby," Jayne responded.

Rae frowned at his response. She began to feel wave of guilt crash into her.

"Why? What's it to you?" Jayne questioned.

"Nothing," Rae responded immediately, making Jayne suspicious of her, "I mean, he's really secretive. He doesn't talk a lot about his life - just the ship and the Matrix."

Kid entered, unexpectedly, asking out of breath, "Who? Neo?"

Rae nodded before Jayne asked, "Why are you so out of breath?"

"Aw, it's nothing," Kid said, waving his hand to cool down his face. "Morpheus was training with me when Link told him Commander Lock found out how close we were to Zion. He demanded that we come back."

Jayne mouthed an 'oh' while Rae's eyes widened, asking, "We're going back to Zion?"

Kid nodded and Rae continued to ask questions. "So that means Neo's girlfriend -Trinity...? - will be there?"

"Yeah. Why, what's going on?" Kid asked.

Rae groaned. "I think my first time in Zion, I'll get my ass kicked."

Jayne and Kid looked at each other, confused, as Rae left, heading back to her cabin.

"We'll arrive in Zion in about two hours!" Kid called to Rae.

--  
Trinity was beginning to remember some of the kids' names in her class. Luckily, Zion's high school, unlike her Matrix one, she only had one class. It was easier to manage like that but it was horrible because she had such an awful group of children for a class.

Their practical jokes have eased up since one of her many lectures about discipline. So far, as Trinity was aware of, they had switched their names multiple times during class, put tacks on her chair, told her she hadn't assigned homework when she had, made her think they hadn't learned certain concepts (just to get out of a test), insulted and embarrassed her many times during class, and so many other things.

Today, Trinity ignored most of their pranks and continued her lesson.

"So to conclude this lesson, the Matrix is nothing more than a computer generated dream world, designed to keep up under control in order to change a human into... basically a battery," Trinity said, realizing this was the same thing Morpheus told her when she was first unplugged.

All the students stared at Trinity, some looking bored, others looking intrigued. She looked at the clock, noticing they only had four minutes left. She didn't know what to do- they never had any extra time before the end of class.

"Umm... are there any questions?" Trinity asked.

One boy with dirty blonde hair falling over his eyes raised his hand. Trinity called on him while his stretched out to the middle of the aisle, revealing his long legs covered by sweatpants. "Uhh, the machines must have been pretty messed up to do that," he said while yawning.

"That's not a question," Trinity pointed out.

"Yeah. I'm just saying." He shrugged.

"Are there any _questions_?" Trinity asked.

Nobody said anything so Trinity changed the subject. "You don't have any homework tonight. Tomorrow, we'll discuss the artificial intelligence in the real world, so if you want to ask anyone about it for prior knowledge, that'd be good," Trinity said.

The teacher from the next room opened the door to the conjoined classroom, drawing Trinity's attention. She walked over the teacher while other students turned their chairs to chat with their surrounding classmates.

Nat, the girl closest to the door of the other class, listened to Trinity and the teacher's conversation, hearing whispers that the Nebuchadnezzar would be arriving at approximately one-fifty. Nat looked at the clock; that was in five minutes.

Trinity smiled, returning to her desk and gathering her things, she told the class they had to go immediately after the bell rung.

At exactly 1:50, the bell screeched, reminding Trinity of her alarm clock on the Neb, which she would soon hear again. Trinity dropped off several books at her apartment and almost ran to the docks. She arrived almost one minute after they landed.

She waited with Zee, who was also at the docks, until the door opened completely and Trinity and Neo saw each other. They held their gazes for only a second before Trinity ran to him and jumped on him, causing Neo to fall back onto the ramp. He didn't really notice, he just kept hugging Trinity.

"Neo! I missed you so much," Trinity cried into his shoulder. She was grinning and also crying.

Neo responded by saying, "I missed you too, Trin."

They were still hugging, lying down on the ramp. Neo didn't mind until Rae came out of the ship, accompanied by Jayne, who stared at the couple. Neo wasn't sure if Rae was mad, jealous, or happy for him. He ignored Rae's emotions and asked Trinity, "Where's Lily?"

"She's still at the day care center. We have to get her in about an hour."

Neo nodded, there was a grimace on his face and Trinity wondered, "What?"

"Listen, I have to tell you some things. You might not like it, but you have to know," Neo said.

Trinity looked scared. "What is it?"

"Come on, I'll tell you over here."

Neo helped Trinity up, although she didn't need it, and walked her over to solid ground. Rae was only about ten feet away from them, talking to Jayne and watching Link and Zee go somewhere and Kid pointing to something at another dock with Morpheus by his side.

"What's going on, Neo?" Trinity asked, fearfully.

Neo dropped his bag and took Trinity's hands. "You won't be able to come back to the Neb… The Oracle told me that the council isn't going to let you because I didn't have enough evidence of the nearing end of the war."

Trinity sighed. She had a feeling this would happen. She nodded and Neo went on, "the second thing. Okay, you aren't going to like this, but will you promise you won't get mad?" Neo asked.

She thought for a second. "Yeah, I promise," Trinity said.

"Okay. We unplugged a girl, Rae," Neo nodded toward her, and Trinity turned to look at her. She noticed her tiny figure and her head covered by a dark blue knit hat. The girl's clothes didn't fit her and only made her look thinner. Trinity raised an eyebrow, now curious as to what Neo had to say about her. "So we had a little argument. And then, I don't know. She _kissed_ me." Neo bit his lip as Trinity's brows furrowed and she ground her teeth.

"Did you kiss her back?" Trinity demanded, sounding more annoyed than mad.

Neo didn't respond. He stared at her with guilty eyes.

Trinity sighed and rubbed her forehead. "You kissed her. Ugh, Neo!" She yelled, only loud enough for Rae and Jayne to hear.

"Wait. _You_ kissed Neo?" Jayne asked, skeptically.

Rae nodded and looked back at Neo and Trinity.

"You didn't..." Trinity started.

"What?" Neo asked.

"Did you do anything _else_ with her...?" Trinity asked quietly.

"What? Trinity, of course not! I felt bad enough after kissing her; I wouldn't ever... have sex with her or anything," Neo said, almost cringing. "She's like, half my age," he muttered.

"Trinity, I really am sorry. If I could take it back, I would." Neo said.

"I know," Trinity replied.

"Are you mad?" Neo asked.

"No. I mean, it's not like I want you to do it again, but I'm not mad," Trinity said, being enveloped in a hug by Neo.

He kissed the top of her head, whispering "I love you" into her hair.

Trinity smiled. She suddenly pulled back. "How old is she anyways?"

Neo looked down. "Sixteen," he responded.

"_Oh, God_." Trinity laughed.

Neo chuckled too. "Do you want to go back to the apartment for a little while before picking Lily up?" he asked.

Trinity nodded. Neo picked up his bag and put an arm around Trinity's waist, walking with her towards their home.

Kid caught Rae staring after them.

"C'mon, Rae. We have to get you registered as a Zion citizen and then get you a place," Kid said.

Rae followed Kid, and as wrong as it was, she secretly wished she was Trinity at the moment.


	12. Chapter 12

Whoa. I'm so sorry for the long wait. You wouldn't believe how busy I am!  
Thank you all so much for your reviews. They are greatly appreciated!

"_A world in myself/ Daydreaming admiring being/ Quietly, open the world/ I hear the time of the starry sky/ Turning over at midnight" Group Four, Massive Attack_

Disclaimer: I don't own the Matrix.

Chapter 12

* * *

"So you're sure you aren't mad or upset or anything?" Neo asked while closing the door to their apartment.

Trinity shrugged. "I guess not… except I was just thinking about that kiss and you, Neo, were cheating on me," she said coolly.

Neo sighed, knowing she would always pull the 'you cheated on me and kissed another woman' card when she wanted something to be done her way.

"I'm only kidding, Neo. No need to get upset," Trinity said, moving closer to him.

"I know that. I'm just upset because I don't want you to think I don't love you any less," Neo said sadly.

"Oh. Neo, of course I don't think that," Trinity said softly, taking Neo's hands from his pockets and holding them in her own.

"I love you," Neo said, leaning in to kiss her. Trinity backed away, causing Neo to stop.

"What?" He asked.

"You think I'm going to kiss you after you were just off with that Rae girl?" Trinity asked angrily.

Neo stared at her, his eyes were wide and his eyebrows raised. _Is she serious?_ he thought before Trinity started to giggle.

"Oh, I'm only kidding," she said, laughing more.

She reached to up actually kiss him this time. When their kiss ended, Neo said, "You know I'm not sure I like what Zion is doing to you."

Trinity laughed again and said, "Come on, we should go get Lily now."

Neo smiled and nodded, following Trinity out of the room.

--

"Hmm. Room 204 W… that's pretty far," Kid said to Rae.

They were walking slowly down one of the many corridors, reviewing Rae's paper work she had just received.

"_Really_?" Rae said sarcastically.

"Yep. I've never even been down here. You're pretty unlucky to have gotten this place," Kid said.

Rae glared at him. She was tired and was in no mood to listen about her apartment that was 'pretty far' away.

"All I'm saying is, most people get placed a little closer to… civilization," Kid laughed.

Rae scoffed and walked faster, making Kid have to jog lightly to catch up again.

"It's just down this corridor, don't worry."

"I'm not worrying about anything," Rae responded.

"I never said you were. I only said not to worry," Kid said.

"Whatever," Rae muttered.

They walked in silence for about another five minutes before Kid suddenly yelled "Wait! Wait. We already passed it."

"No we didn't," Rae said, sounding annoyed.

"Yes, we did! This is 218 W and you're 204. Let's go back," Kid said, already turning around.

Approximately another five minutes later, they found Rae's apartment. Kid jammed the key inside and twisted the heavy metal wheel.

Rae stared at the inside of her apartment- furnished and clean. Kid checked to make sure all the appliances and electronics were working (which they were) and to make sure she wasn't ripped off.

Rae offered him a glass of water, which he took, and they sat together at the small metal table in the kitchen.

"Rae?" Kid asked.

"Mhmm?"

"What's going on with you and Neo?" Kid asked, tilting his head to the side.

Rae felt her heart beat go faster and a smile flashed upon her face. "Nothing, really. Don't tell anybody this, okay?" Kid nodded and Rae continued, "The day we were arriving in Zion, I kissed Neo."

"You what?!" Kid shouted.

"Yeah, I knew that'd be your response," Rae murmured.

"Oh! So that's why Trinity was like that on the docks. Hmm… that makes sense now," Kid said.

"She was like what? Do you think she's mad at me?" Rae asked, now very anxious.

"Eh. I really can't tell. Only she and Neo know. And I'm neither one of them, so I really can't help you," Kid said.

"Gee. Thanks," Rae said sarcastically.

"So do you like him? I mean, if you kissed him, you must have thought _something_ was there," Kid reasoned.

"Well, sure. I don't think I'm in love with him, but yeah. He's attractive, nice, and from what I've seen, he's pretty emotional- in a good way."

Kid raised an eyebrow. "Wow. That's a little creepy," he muttered.

Rae punched his shoulder playfully.

"You're going to the council meeting, aren't you?" Kid asked after a minute.

Rae nodded. "What's it about, anyways?"

"Oh, a lot of things," Kid responded. "It's mostly about whether you're going to stay on the Neb and if Trinity is coming back on."

"Oh," Rae said quietly. _That must mean Trinity will be there. Damn_, Rae thought.

--

Almost two hours after Rae and Kid talked, the two of them were summoned to one of the smaller conference rooms.

Rae was standing by Kid and Morpheus, staring nervously at the door. Neo and Trinity walked in, carrying their daughter, Lily. As Trinity entered the room, she spotted Rae, making eye contact with her before looking away.

Rae gulped and took her seat, copying the rest of the humans in the room.

She sat next to Kid, on her left, and Trinity, on her right, separating her and Neo from sitting next to each other.

_This is awkward…_Rae thought.

"Thank you for coming on such short notice. The council and I greatly appreciate it," Councilor Hamann started. "We want to clarify any confusion to what will be happening. These are new circumstances to us all and the council thought it would be best to make a decision together."

"Rae," Councilor West said.

Rae looked up immediately, unsure of what to do.

"Stand up," Trinity whispered.

"What?" Rae asked, still confused.

"Stand up," Trinity said again quickly, enunciating each consonant.

Rae stood up slowly.

"Now, no need to be nervous," Councilor West said. "Because we do not know much about your capabilities upon the Nebuchadnezzar, we are allowing you to stay aboard."

Rae smiled. She liked it on the Neb; her crew was nice and aside from the coldness, it was comfortable.

"Trinity," Councilor Dillard smiled, "The council is well aware of your want to go back on a ship. We want you to stay in Zion until more information from the Oracle is given."

Trinity nodded and sat back down. Moments later, they were all dismissed from the meeting.

Trinity followed Neo out, before stopping when her name was said.

She turned around to face Rae. "Yes?"

"Uhh… Trinity, I want you to know that I'm sorry for… what happened between Neo and me," she said, awkwardly.

Trinity's expression eased and Rae smiled, relieved. "It's fine, Rae. Besides, I blame Neo for all that happens."

Neo turned around and pouted. Lily laughed at her father and Trinity did the same.

Rae showed a brief smile and ran ahead of them to catch up to Kid.


	13. Chapter 13

Whoaa! I went onto the Matrix fan fiction archive and I was so surprised! There were a ton of new stories up. Good for you guys!

"_I believe in self-assertion/ Destiny is like diversion/ Now it seems I've got my head on straight/ I'm a freak without provision/ Seems I've made the right decision/ Try to turn back now, it might be too late…" Stay Home, sElf_

Disclaimer: I don't own the Matrix.

Chapter 13

* * *

"So, when are you going back?" Trinity asked over the kitchen table.

Neo was feeding Lily cheerios while eating some fresh fruit.

"Tomorrow," Neo responded. Trinity nodded and Neo saw the hurt look in her eyes.

"Don't worry. You'll be put back on the ship sooner or later," he said.

"Yeah, but 'sooner' isn't possible and 'later' might be too late," Trinity said, sighing.

Neo decided to change the subject. "How's your job as a teacher?"

"It's alright, I guess," she replied.

"Oh?"

"Yeah, some of the kids are complete jerks but there are a couple decent ones."

Neo smiled and refilled Lily's bowl of cheerios. Lily grimaced causing Neo to chuckle and say, "eat up, Lil'. I'd much rather have those than goop everyday."

Lily picked up another cheerio and put it in her mouth.

Trinity got up and grabbed a knife from the drawer, grabbed an apple from the fruit bowl on the counter, and started to cut it into thin slices.

After a small pile of apple slices was made, she put them on Lily's plate, saying, "here you go, sweetie."

Lily smiled and took a slice gratefully.

Neo sighed heavily and Trinity asked, "what?"

"Trin, you know her so much better than I do. She can say 'mama' and she isn't even close to saying 'dad'."

"Neo, it's only normal. I see her every day now and you don't. She still loves you. It'll just take her longer to be able to say everything that applies to you. Besides, you were at least there to hear her first word and it was directed to you. Doesn't that count for something?" Trinity asked.

"Of course it does," Neo replied. "I just wish I could be here with the two of you."

"I wish that too," Trinity said, placing a hand over Neo's.

"Daddy?" Lily whispered from her high chair.

"What?" Neo said, not even realizing his daughter actually addressed him.

"Daddy," Lily said again.

Neo whipped his head towards her and a grin spread on his face.

"You, Lily, are becoming very well known for your unpredictability," Neo said in a matter-of-factly tone.

--  
The rest of the day passed quickly, to all of their surprise.

Trinity was lying on her and Neo's bed, stomach towards the ceiling, breathing heavily. Neo was tucking Lily in, taking, for what Trinity thought, an eternity.

Trinity stretched out her arms and legs and shut her eyes. She could've fallen asleep at that moment if Neo hadn't pounced on her.

Trinity half laughed, half yelped, only to be cut off by Neo's hand over her mouth.

"I finally got Lily to sleep," he said proudly, "now don't wake her up. We have other things to do."

Trinity understood what he meant and raised her brows. "What do you have in mind?" She asked, seductively.

The corners of Neo's mouth raised and he leaned down to kiss her deeply.

Trinity moaned into his mouth. "I've missed this," she said after their kiss broke.

Neo nodded and kissed her again, passion dripping from their tongues.

"Daddy!" Lily screamed from the other room.

Trinity cursed under her breath after Neo got off her to tend to his daughter.

He walked into her room, tears streaming down her red face. "Yes, my darling?" he answered.

Lily stood in her crib and pointed to a stuffed animal that fell onto the ground.

Neo reached down to get the bear and handed it to Lily. "You're welcome," he said.

Lily grinned, showing her growing in teeth.

When Neo returned to Trinity she asked, "What did Lily want?"

"She dropped her bear or something," he responded.

Trinity mouthed an 'oh' as Neo plopped down next to her on the bed.

He draped an arm over her stomach. Trinity asked, "Would you like to continue from where we left off?"

Neo didn't respond, he only rolled over towards her and starting kissing her neck.

Not even 10 seconds later, they heard Lily scream again. "I'll go," Neo volunteered.

Neo flicked the light switch to dim and found Lily again, red faced and crying. "What's wrong, hon?" he asked.

He looked under her around the room and under her crib but didn't see any fallen item. He picked her up, checked to see if she needed her diaper changed –which she didn't- then carried her into the next room.

"What's wrong?" Trinity asked.

"I don't know. She won't stop crying," Neo said.

Trinity took the child from Neo, and also checked her diaper, then went into the kitchen and offered her water and a grape. She rejected both and was still crying loudly.

Neo took Lily back and sat with her on the bed. Trinity followed and propped herself up against the cement wall, watching Neo's attempt at calming Lily down. She watched as he whispered something in her ear and she -almost magically- stopped crying. A couple minutes later, she was fast asleep again.

"She'd better sleep with us for a little while," Neo suggested.

"What did you say to her?" Trinity asked.

"I only said 'I'm not leaving now'. I don't really understand how that stopped her crying, but it worked, so I'm not complaining," Neo said.

Trinity smiled warmly and said, "See? I told you she loved you."

Neo laid their daughter in between them on the bed and we watched her curl up with the blanket.

"Do you mind if I smuggle her onto the Neb tomorrow?" Neo jokingly asked.

"Go ahead. Just make sure you're hundreds of miles away before Lock finds out," Trinity laughed. Neo did too.

"I can probably get you on too," he said, this time only partly joking. He wished he could, but knew the consequences would be much worse.

Trinity laughed again. She thought it was physically impossible to do that; if only she knew what plan Rae was thinking of, at that very moment, to do that exact thing.

Ooh. Interesting again? I hope so. Hopefully the next update will be soon, but I'm really not sure. Reviews are always nice, if you can do it. Thanks to everyone who did so far.


	14. Chapter 14

"_Don't be afraid/ Open your mouth and say/ Say what your soul sings to you/ Your mind can never change/ Unless you ask it to..." –What Your Soul Sings, Massive Attack_

Guhhhh -drawls- . I bought a Massive Attack album the other day (100th Window) and oh my god, I love it. I'm usually not one for the soft and slow music, but Massive Attack is one of my only exceptions.

Also, thanks for everyone's reviews and support. I really, really appreciate them all!

Disclaimer: I do not own The Matrix

* * *

The day arrived, feeling earlier than usual. Trinity, Neo, and Lily once again arrived last to the docks.

"Once again, I will tell you that we'll be careful and come back soon," Neo said.

"You better," Trinity teased.

"Alright, I'll see you soon," Neo said.

"Bye. Love you," Trinity sang.

"Bye. Love you, too. I love you, Lily," Neo said.

"Bye, daddy!" Lily giggled.

Neo said his goodbye again and walked onto the ship. They were only waiting for Rae now.

"Shit, shit, shit!" Rae muttered as she ran down the stairs to the docks. She was up all night thinking about everything that had happened since she was unplugged – learning about the Matrix, her visit to the Oracle, being shot, the Smith program…- and didn't get any sleep until 'sunrise' came.

Trinity and Lily left, taking the stairway, passing Rae on the way up.

"Whoa, Trinity," Rae panted, "did the Neb leave yet?"

Trinity laughed. "No, they're waiting for you."

"Oh, good," Rae breathed, "I was afraid they left already!"

Trinity laughed again after Rae started running. _They would never just leave her here,_ Trinity thought.

"Rae, where were you?" Link questioned when she finally got aboard the ship.

"…Just running late," she said, heading for her cabin to drop off her bag.

Over two hours since they left Zion, Neo, Rae, Kid, and Jayne were all busy in the core.

Rae and Jayne were in a training simulation that Link created, being overlooked by Neo and Kid.

The ship jerked -causing both Kid and Neo and hold on tightly to the operator's chair- then came to a sudden halt. Then lights in the core shut off, only the Matrix feed screens illuminating the walls.

They were still for a moment before Neo told Kid to unplug Rae and Jayne while he moved to find the intercom to ask Morpheus or Link what was happening.

"It's nothing much. Bring everyone down to the mess hall, we'll meet you there," Link responded.

Neo obeyed and told his crew to follow. The lights came back on, very dim, allowing them to see only a little bit. Minutes later, Link, Morpheus, Niobe, Sparks, and Ghost joined them.

Neo was surprised to see them, but nodded his hello.

"Rae, Jayne, this is Niobe, Ghost, and Sparks of the Logos," Morpheus said, gesturing to each person.

"As you have probably been wondering, I have arranged this meeting for a purpose," Morpheus said, "You all know Trinity has been taken off the ship, but what you may not know is, she is one of the most important people to help the ending the war. I believe that if we can get her back aboard a ship, we will finally be able to end this."

The group was silent for a few moments until Ghost asked, "How do we get her on the ship?"

"I don't know. That's our first problem," Morpheus replied.

"I have an idea… But you aren't going to like it," Rae said quietly.

"Tell us," Morpheus said.

"Alright," Rae said, "So, first we'll start out by…"

--

Everyone left the mess hall after Rae's plan was confirmed, except for Neo and Ghost.

"You really think this'll work?" Ghost asked.

"It's dangerous, I'll admit to that," Neo said, "But we don't really have any other choice."

"Yeah," Ghost muttered.

Niobe peeked her head into the room and said to Ghost, "We have to go. Morpheus wants to do this as soon as possible."

"Alright," Ghost said. "Nice talking to you, Neo. I hope everything goes okay."

"Thanks. Nice talking with you, too," Neo replied.

"Morpheus wants you up there with him, Neo," Niobe said.

Neo nodded and left to meet Morpheus in the piloting station.

"Are you ready?" He asked after the Logos were almost three miles away.

"How many sentinels will there be?" Neo asked.

"I'm estimating about three to twelve," he said, "But I can't be sure."

"That's a wide range," Neo said monotonously.

"That's why I said I can't be sure," Morpheus replied.

"I'm ready," Neo said.

Morpheus pressed a button of the control panel and spoke through the intercom.

"Link, give us as much heat and energy as you can," he said.

"Are you sure you want to do this?" Link asked.

"Yes," Morpheus automatically said.

"Okay, sir. All power units on…" Link said. "And the heat is on as much as it can go," he added after a minute.

Neo squinted at the bright light he wasn't accustomed to. They waited for about ten minutes before Neo saw the sentinels coming towards them.

"We can blow the EMP now," Morpheus said.

"No," Neo replied sternly. "This will work… it has to."

They watched the sentinels move around the large windshield before one of their enormous tentacles expanded, shooting out a laser, cracking the windshield.

"Shit!" Neo yelled. "Come on, Morpheus."

They sprinted down the hallways and climbed down the latter into the core with Link.

"Charge the EMP- now!" Neo breathed.

Rae, Jayne, and Kid ran into the core with them.

"They're breaking into the cabins too," Kid yelled.

Rae screamed when a chunk of metal fell to the ground on the other side of the room and a sentinel swooped in. It stared menacingly at them and began to move towards them lethally.

Neo didn't wait another second; he ran towards the EMP and twisted it, killing the machine as it reached out towards him.

It was silent. Neo turned to face the group and slid down to the ground, leaning against the operator's chair. He breathed deeply and watched the others recover.

They were all sitting up now, except for a figure behind everyone.

"Rae?" Neo whispered. Morpheus looked at him then to Rae. "Rae?" Neo said again, this time loudly.

Kid crawled towards her and moved her onto her back, checking her pulse.

"She's okay," Kid said.

"Probably just passed out from the shock," Link added.

"Take her down to the med bay," Morpheus ordered, "I'm going to contact the Logos."

Link and Kid carried Rae away and Morpheus went back to the piloting station.

"Are you alright?" Jayne asked.

Neo nodded, shoving the sentinel's tentacle away from him.

"Yeah. Are you?" He asked.

Jayne nodded. "I'm going to go see what else was damaged," he said.

When Jayne left, Neo sighed and hit his head against the back of the chair. He looked around himself, seeing pieces of metal everywhere.

"It seemed like a good idea earlier," Neo said to himself.

* * *

Whoo! Chapter 14 is done! I hope you liked it. Reviews are cool if you have time. )


	15. Chapter 15

Hey. Sorry if the last chapter was confusing. Hopefully everything will come together in this one. Listening to Massive Attack (as always) so if it weren't for my screwed up computer speakers, I'd be very happy. Aw well.

I'm really sorry for all the short chapters. I believe it is physically impossible for me to write a long one. I feel like I'm totally ripping you guys off, but I really do appreciate those who read and/or review them!

Disclaimer: I do not own the Matrix. (I wish I did…)

"_Everybody knows we're ruining this town/ Why'd you go and bring us all down/ It's all just for show/ The sights consume the sound" Dog You Are, sElf_

* * *

"Why the hell didn't you blow the EMP before?" Ballard, captain of the Caduceus, asked.

"It was err… part of a plan," Kid said awkwardly.

"I don't understand," Sonja, the Caduceus' operator, said.

The Nebuchadnezzar, Logos, and Caduceus' crew were standing closely together on the surface. The Logos and the Caduceus found each other earlier and came back together to help the Neb after they called.

"Well it's a long story, but in a nutshell, the Oracle told Neo he needs Trinity to help him end the war and this was our plan to get her back aboard," said Jayne.

"How would destroying your ship help get Trinity back on," Bane asked, now very confused.

"We figured we could sneak her on in Zion while doing repairs after the sentinels attacked. And we had to lure them here so we tried to use as much power as possible," answered Kid.

"Hmm… that's smart," Ballard replied. "Listen, the council or any other crew doesn't have to know about this as long as you make sure this works."

"It will." Morpheus assured.

"Anyways, we'll help you out as much as we can," said Ballard. "Malachi, why don't you get some metal sheets we can cover all these holes temporarily?"

"Yes, sir," Malachi responded, running to his ship with Ghost and Sparks to get the makeshift covers.

"Where's Neo?" Bane asked, sounding gruff and aggravated.

"He's still on the ship…," said Link, not understanding Bane's aggravation.

Bane turned on his heels and stalked off towards his ship.

"Creep," Kid muttered. Jayne laughed and also ran off towards the Caduceus to help carry repair items.

"What happened?" Rae asked groggily, trying to sit up on the table in the med bay.

Neo was only a few feet away from her, leaning against the wall, arms crossed, and expression tense.

"After the machines attacked, you passed out," he said quietly.

"Is everything okay?" Rae asked, noticing Neo's expression.

"I guess," he responded, "I'm just not sure if this will work anymore."

Rae hopped down from the table, gripping the sides for support. She flashed her white teeth at him and said playfully, "You have self esteem issues!"

He raised an eyebrow, trying to hide a smile of his own.

"Let's go," he said, "They need us out there."

Rae nodded and practically skipped off the ship, meeting with her crew.

"We have a lot to fix up here, but we don't want to repair everything as we still want to get to Zion," Morpheus informed them.

Neo and Rae confirmed and Morpheus commanded them to help start repairs.

On one side of the ship, Neo found Bane, Niobe, and Jayne trying to drag a sentinel out of one of the unoccupied cabins. He pulled himself up into the cabin about five feet from the rocky surface and walked around Niobe and Jayne to help pick up the sentinel from Bane's side.

He reached under the sentinel's outer core to get a better grip when Bane grabbed his wrist, revealing the many lines cuts on his arms and enabling Neo to move.

Neo gasped and Niobe and Jayne looked up, stopping their muttering.

"Bane, what happened to your-," Niobe said, getting cut off by Bane.

"Don't touch there. You might get a nasty shock," he said, smiling wickedly.

Niobe said her question again, this time finishing it. "What happened to your arm?"

"Nothing. I'm perfectly fine," said Bane as he rolled down his sleeves, covering his arms.

Niobe, Jayne, and Neo eyed him suspiciously but then dismissed it and continued to pull the sentinel out of the room.

In a few hours, the Neb was ready to go back to Zion. They had put in a plexiglass windshield that would keep up until they got permanent repairs done in Zion. Most of the holes were covered except for the smaller, trivial ones.

"The Caduceus is going to follow you into Zion. We'll stay out here and wait for you. When Trinity is back aboard, we can go from there." Niobe said.

The other captains agreed and set off.

--

Trinity once again watched her class come in, chattering and doing their hair and makeup.

"Alright, alright, you know what to do every morning. Opening Question is on the board, do it in your notebooks," said Trinity.

Each morning, an opening question would be put on the blackboard to start off their topic of the day. Today's topic would be about someone's abilities in the Matrix and more about Zion's history in the war.

Halfway through class, they were still discussing the rules of the Matrix.

"Say someone was in the Matrix and then had a heart attack or something, would they have a heart attack in the real world too?" A girl asked.

Trinity thought about the question for a moment. "I'm really not sure," she said. "It's never happened before so I can't give you an exact answer."

A knock on the door interrupted everyone's attention. Trinity said, "Come in." before Rae walked in nervously to Trinity's desk.

"Rae?" Trinity said, unsure of why she was here.

"Trinity, I can't explain everything now, but you have to come with me," she said.

"I'm in the middle of a class."

"I know, but it's important," said Rae.

"Okay," Trinity said. Rae started walking back towards the door. Trinity followed behind and said to her class, "Just do other homework or read a book until I come back."

Once out of the door Rae muttered, "They're going to be doing that for a while then."

"Rae, what's going on?" Trinity demanded.

"We're getting you back on the Neb so we can end the war."

"What? How can we do that?" Trinity asked, trying to keep up with Rae's fast pace.

"Let us take care of that," said Neo, running up from behind her, slipping an arm in around her waist.


	16. Chapter 16

"Day's dawning, skins crawling/ Pure morning/ A friend in needs a friend indeed/ A friend who'll tease is better/ Our thoughts compressed/ Which makes us blessed/ And makes for stormy weather," Pure Morning, Placebo

* * *

"Neo, please, tell me what's going on," pleaded Trinity. The three of them stopped. Rae looked annoyed at the interruption but Neo and Trinity ignored her.

"Alright, I didn't tell you this, but the Oracle told me that I would need your help to end the war," said Neo, for what felt like the hundredth time.

"Okay, I'm confused. But before you explain any further, let me ask you this: why are you in Zion?"

"We purposely destroyed our ship and now we're taking you aboard whether you like it or not," said Rae tiredly.

"What? This is crazy," Trinity exclaimed.

"Yeah, I realized that the moment after I explained it to everyone the first time," replied Rae.

"Then no wonder its crazy," muttered Trinity, looking away from the young girl's gaze.

"What's that supposed to mean?" Rae snapped.

"Hey!" Neo hissed. "I'm in no mood to break up a fight, so you two better stop. Besides, we don't want to draw any _more _attention towards us." He huffed, realizing how much of a pain it was to be 'the One' in Zion.

"Fine," Trinity murmured. "How are we getting Lily on the ship?" she asked, picking up their pace again.

Neo stopped once more, turning himself to face Trinity and taking an extra step closer to her. "Trin, she can't come," said Neo, softly.

_"Excuse me?"_ Trinity asked in disbelief.

"It's too dangerous for her," Neo said.

Trinity shook her head. "No, Neo, you might've managed to leave her, but I can't."

"Trinity, you have to," he said firmly.

"Who's going to watch over her?" Trinity asked.

"Link is asking Cas and Zee right now."

"Neo, you're pressuring me into something I don't want to do," said Trinity, her voice showing obvious pain.

"I know. And you don't know how sorry I am for that."

"Please. Don't make me leave her," Trinity begged softly.

"Trin, the sooner we do this, the sooner we can live in peace with Lily. Don't you want her to live without fear?" Trinity nodded and wiped her wet eyes.

Rae now felt a bit guilty for the argument she and Trinity just had. "We should go now. People are starting to stare at us," Rae added. They moved quickly, ignoring everyone who came close to them.

"The Caduceus is repairing the ship with us. They know about the plan; they're here to help us," Neo whispered into Trinity's ear. She recognized the Caduceus' crew as she, Neo, and Rae got closer.

Behind the ship was a large crate on a platform cart. Neo led Trinity towards it and said, "Here, get in, and don't come out until I tell you." Trinity stepped into the crate cautiously, ducking down, wrapping her arms around her legs and burying her head in the space between her knees and chest. Neo leaned into the crate and said, "I'm just putting some metal sheets over you in case somebody looks inside. Don't worry, they're not heavy." Trinity barely nodded and then felt the sheets sit lightly on top of her. The lid of the crate closed, surrounding her in complete darkness. Neo pushed the cart slowly at first, then picking up his pace to a light jog. He headed towards the boarding ramp and Trinity felt a sudden stop. She started to panic at first, thinking they'd been caught, and then she heard Neo's voice. She strained to her him.

"What is that?" a man asked. It was Lock, Trinity recognized the voice.

"Just some scrap metal to repair one of the holes a sentinel made from inside," Neo explained.

Trinity didn't hear a response from Lock, but only imagined him glaring at Neo. She suddenly saw light creep into the crate and heard the sheets being tampered with. She steadied the bottom sheet above her and ceased her breathing. She knew Lock was examining the contents in the crate. Trinity finally continued her breathing when the darkness returned to her again.

She slid backwards while going up the ramp and thought about how they could get her to a safe place on the ship, while still in the crate, without anyone's knowledge. Once more, she saw the light come to her. The metal sheets were removed from the crate and she looked up to see Neo smiling above her. He offered her a hand, which she took, and stepped out of the crate. "Come on. We can't let anyone see you," said Neo, taking her hand once again, leading her towards their cabin. Neo closed the door and grinned.

"What?" Trinity asked.

"I didn't think this would work," said Neo, stepping towards her and placing his hands on her hips.

"Don't be so happy. We aren't out of the woods yet," Trinity said, sliding her hands up Neo's chest.

"In two hours we will be."

"_Two_ hours, you say? I think we can get something done within that time."

"Oh yeah? What were you thinking of?" Neo asked, well aware of Trinity's hint.

She stood on her toes and kissed Neo deeply. "I hope your friend Rae there won't interrupt us," said Trinity as she broke their kiss.

Neo shrugged. "I'm sure she could learn something." Trinity laughed and continued to kiss him.

About an hour and a half later, Rae knocked on Neo and Trinity's door. Not waiting for a reply, she opened it and found Trinity lying on her stomach and Neo propped up on his elbows beside Trinity, blankets covering only their lower halves, talking. "Whoaa!" she said, turning around, her back now towards them. "Umm, just coming to tell you that we're, uh, leaving in a few minutes and, ahem, Morpheus needs you, er, Neo in the cock. Shit, uh, cockpit."

After Rae closed the door Trinity burst out laughing at Rae's reaction. Neo laughed too. "Well, today will be awkward." Trinity couldn't have said it better herself.

Neo and Trinity both dressed and headed down to the cockpit, although only Neo was summoned.

"We're getting ready now. The Caduceus will be following us back to the Logos," Morpheus informed. "I don't know what you plan to do after, Neo, but I will only assume it's something good."

Neo knew what he had to do nest, but didn't dare say it… yet. Instead he only followed Trinity's actions and prepared for their departure.


	17. Chapter 17

"_I can't remember when it was good/ moments of happiness elude/ maybe I just misunderstood/ all of the love we left behind/ watching the flash backs intertwine/ memories I will never find" Falling Away With You, Muse_

Oh, my! Sorry for such a long wait. I haven't been in the mood to write for a while.  
I guess I won't bore you with a long author's note, so here you go.

Chapter 17

* * *

At exactly 2:30 the school bell rang and the students rushed out. Three boys, who've suffered Trinity's wrath, sprinted down many flights of stairs down to Commander Lock's office, Nat following right behind them. Unlike the boys, Nat liked Trinity. She didn't know her well, but for the past couple weeks they'd gotten along fine. The boys rushed into Lock's office, not waiting to be escorted in, only to interrupt Lock and Councilor Hamann's discussion.

"What's going on, boys?" Councilor Hamann asked. Nat ran in too, bumping her head into one boy's back.

"Uhh, well," the first boy started.

"Trinity left our class with some girl who's on the Nebuchadnezzar!" the second boy blurted out.

"Dude, shut up!" the third boy hissed.

"Sorry," muttered the second kid.

"What?" Commander Lock growled, standing up and punching his fists on his desk.

"Commander, please. And you're sure this girl who came to your classroom is a fighter aboard the Nebuchadnezzar?" the Councilor asked.

The first boy nodded. "We saw her when they first docked. We didn't recognize her at first but by the end of class we did."

"Goddamn it! I should've known they would try something like this!" Lock violently yelled. "And I was there the whole time! Must've snuck past me those…"

"Excuse me, sir," Nat squeaked, "I think what Trinity did was necessary for our survival." A low growl escaped Lock's mouth before ordering Nat and the boys away.

"Lieutenant!" Lock yelled. A tall, plump man, no younger than thirty five, walked into the room, responding to his Commander's call, bumping shoulders with Nat, who was on her way out of the office.

"Yes, Commander?" the lieutenant asked, standing up straighter and tensing his arm muscles.

"Find some of my men and see if the Nebuchadnezzar left yet," ordered Lock.

"Yes, sir," the lieutenant said, turning to leave. "Sir, what should I do if they didn't leave yet?"

"Get Captain Morpheus and bring him here!" Lock yelled.

"Yes, sir."

Lock mumbled something and shuffled through the papers on his desk. "Commander Lock, how do you know Trinity status on a ship isn't for the best?" Councilor Hamann asked.

"Councilor, if it were for the best, then I'd assume you wouldn't have taken her off the Nebuchadnezzar in the first place," Lock replied coolly. Councilor Hamann remained quiet and thought about Lock's words.

"Commander!" the lieutenant yelled, moments later, walking into Lock's office. "We asked one of the mechanics at the docks and he said they left a couple hours ago."

Lock narrowed his eyes and ordered everyone away, saying he needed time to think about the situation he was in.

Nat was waiting for Councilor Hamann outside Lock's office.

"Councilor!" Nat yelled, running to him as he exited the room.

Hamann bowed his head and Nat continued to talk.

"Is Trinity in trouble?" she asked.

"If she comes back without ending the war, then yes, I would assume so. If they do finish this, then I would think Zion would be very forgiving," said the councilor, matter-of-factly.

"Councilor?" Nat asked softly.

"Yes?"

"Do you believe the war will end?"

"Yes, I believe it will. It must one day. I can only hope I live to see that day," Hamann replied proudly.

"Me too," said Nat, before saying goodbye and walking away towards her home.

As the Nebuchadnezzar made their way through the tunnels, Neo was thinking of how to tell his crew how he planned to end the war. Trinity knew something was wrong but she didn't ask Neo about it. She'd wait until they were alone and he could tell her exactly what was on his mind.

Morpheus and Link set the ship down across from the Logos, leaving enough room for the Caduceus to fit beside them. "This is Captain Morpheus. Everyone report to the mess hall. We'll be meeting the Logos and the Caduceus there in approximately ten minutes," Morpheus said through the intercom. Morpheus gestured for Trinity and Neo to leave while he and Link shut down the unnecessary power.

Trinity climbed down to the middle floor, instead of the bottom, where the mess hall was. "Trinity, what're you doing?" Neo asked when he saw her getting off the ladder.

"Come here," said Trinity, taking Neo's hand and leading him away from the ladder.

They were in the core now, standing several feet away from the operator's chair Rae was sitting in. Her petit, slouched frame was hidden behind the back of the chair as she watched the Matrix code. She knew she should've left the couple alone, but a part of her wanted to know what was going on; so she stayed.

"Neo, what's wrong? Something about this is bothering you, I know it. You can trust me," said Trinity, looking into Neo's glossy brown eyes.

"I know what I have to do to end the war," Neo stated, playing with Trinity's fingers entangled in his.

"What?" Trinity asked.

"You aren't going to like what I tell you."

"Tell me," said Trinity.

"I have to go to the Machine City," said Neo, inhaling sharply.

"I don't understand," said Trinity, confusion evident in her voice.

Rae clapped her hands to mouth to prevent herself from speaking out.

"I don't either. But I know what my senses are telling me and they're telling me to go to the Machine City."

"Then I'm coming with you," said Trinity automatically.

"No. It's too dangerous," Neo said.

Trinity shook her head. "I can't leave you. We'll go together. You need my help," Trinity reasoned.

Neo sighed heavily and glanced around the room then looked back to Trinity face. "Fine," he said after a moment, "but please, tell me you're going to be careful. I can't stand the thought of losing you."

"It's okay. We'll look out for each other," Trinity said, caressing Neo's face.

Neo turned his head to kiss Trinity's palm before he took her into a hug. After a moment, they broke away and went down to the mess hall followed by Rae, who claimed to be in her cabin.

"Thank you all for coming. I know this is… different than usual meetings, but I can assure you, it is both important and necessary," said Morpheus, when everyone was present in the Nebuchadnezzar's mess hall.

Niobe stepped forward, unraveling a large paper and placing it on the table in the middle of them. "I'm not sure what Neo's gonna do or how it could effect this plan, but I figure, if we can get into a position close to a sentinel hideout, we can blow an EMP, stopping hundreds of them from reaching Zion. Now, I know it may sound steady now, but it could turn out disastrous," she said.

"Yeah, it sounds decent," Ballard said. "Neo, you have any idea what to do?"

Neo looked up from the ground. His hand gripped Trinity's harder and she nudged his side.

"Neo?" Morpheus said, telling him to say what was on his mind.

Neo waited a moment longer before saying, "Yes. I know what has to happen. I'm going to the Machine City…"

"_What?_" Sparks scoffed with his jaw dropped open.

"Do you know how crazy you sound for saying that?" asked Niobe.

"Does it sound better to know I'm going with him?" Trinity asked in a tiny voice. All eyes were on her and Neo now, and only until now, did Trinity see the look of worry across Ghost's face.

* * *

A billion thanks to everyone who's been reading or reviewing. You have no idea how much I appreciate it! Reviews are welcome (and awesome) as always...


	18. Chapter 18

"_I'm here again/ A thousand miles away from you/ A broken mess/ Just scattered pieces of who I am/ I tried so hard/ Thought I could do this on my own/ I've lost so much along the way" –Pieces, RED_

* * *

"No. It's far too dangerous. Neither of you should go," said Ghost.

"Wait," said Rae, "why aren't we all going? Why is it so dangerous?"

"We have to go, Ghost," Trinity said softly.

"How are you getting there?" Ballard asked.

A moment of silence was held before Morpheus said, "They can take the Neb. We'll go aboard your ship, Niobe."

"Can someone answer my question?" Rae asked, irritated.

"No. Mine's faster; Neo and Trinity should take it," Niobe suggested.

The three captains nodded

"Alright. Let's get packed and get ready for departure," said Morpheus.

"Hey!" Rae shouted. Everyone in the room turned to her, surprised such a small girl could be so loud. "Before anything else happens, will someone _please_ explain to me what the hell is going on?

Neo sighed. "You all get ready. I'll explain."

The room cleared in a matter of seconds, Trinity being the last to leave.

Rae was still standing in the back of the room, pouting with her arms folded across her chest.

"Rae, sit down," said Neo, who also sat at the table.

Rae obeyed and sat across from Neo.

"So, are you going to explain everything to me?" She asked calmly, unlike the voice he'd heard before.

Neo nodded.

"First off, why can't all of us come?" Rae asked.

"The reason you can't come is because… I don't want you to."

Rae felt insulted. "Why not?"

"Rae, you're just a kid," Neo replied.

"So what? Are you saying if I were older, you'd let me come?"

"No. Even then, I still wouldn't let you."

"Neo, why is Trinity going?"

Neo hesitated with this answer. "Because… Trinity's been in this far longer than you have. She knows what she's dealing with and to be honest, I can't stop her."

"Fine," said Rae stubbornly. "Why is it dangerous?"

"You remember the program, Smith? He's out of control and we don't know how far his capabilities go."

Rae nodded. "Alright. Well, thank you for answering me."

Both Neo and Rae got up from their place on the bench. As Neo headed towards the door, Rae stopped him.

"Neo?"

"Yeah?"

"Promise to come back," said Rae, more demanding than wishing.

"I promise."

"If I ever have a son, I'm naming him after you," Rae said.

Neo was stunned. "Thank you," he said, only now realizing Rae crying and hugging him.

Minutes after Neo had returned to his room to pack with Trinity, there was a soft knock on the door.

Trinity hurriedly answered it, not surprised to see Ghost there.

"Can we talk?" he asked.

"Sure, hold on," said Trinity. She looked back at Neo, who knew what Ghost was about to tell her.

"I'll be back," Trinity said to Neo, as she left the room with Ghost.

They stopped at the end of the corridor, away from everyone in listening distance.

Moments of silence passed as each tried to think of words to say.

"Never thought we'd come this far," said Trinity, stuffing her hands into her pockets.

"Neither did I. Especially to be here with my best friend," Ghost said, a gentle smile on his face.

Trinity smiled too. "Don't you ever wish that we could go back to the time before we were recruited and all we ever did was hang out?"

"All the time," Ghost replied.

"Trinity, since the first day I've met you, I've always thought you were the most amazing person I've ever met," said Ghost.

"Wait. Ghost, don't give me this. I'm coming back. Save yourself from the awkwardness between us for when I do come home," Trinity advised.

Ghost chuckled. "Okay, but one day, I will tell you."

Trinity nodded.

They walked back to Trinity's room together. Before she entered, she said, "I'll see you before we leave."

After Ghost had left, Trinity came back in to find Neo had finished packing and was now staring at himself in the mirror.

"What's wrong?" Trinity asked as she came up to him from behind to wrap her arms around his waist.

Neo huffed. "I just can't believe how fast this is all happening."

"Don't worry. Before you know it, we'll be home in Zion. And we can finally see Lily," said Trinity.

"That's true," Neo said, looking at Trinity in the mirror and smiling at her.

"Are you ready to go?" Neo asked.

"Yeah. It feels strange though."

"What does?"

"Leaving. I've been on this ship for such a long time," said Trinity.

"Like you said, before you know it, we'll be back." Trinity's eyes brightened.

"Let's go. They're probably waiting for us," said Neo. Trinity took his hand, walking with him down to the lower deck of the Nebuchadnezzar.

Meanwhile, Rae was in the mess room, pacing back and forth.

Bane had entered, giving Rae the chills, and getting a glass of water. He sat down at the table and watched her carefully. Several times she had stopped to look at him but when they had made awkward eye contact, she decided to ignore him.

"Why aren't you helping the others?" Bane asked.

Rae jumped, shocked by the sound of his voice.

She didn't want to answer, but knew it would be rude if she didn't. "Morpheus got mad because I wasn't being much of a help, so he sent me in here."

"I see. If you were wondering, I came here looking for you."

Rae stopped in her spot. Her back stiffened and her face twisted. Although she didn't know why, Rae had a bad feeling about Bane. "Why?"

Bane got up from the bench. Rae backed up into the wall behind her as Bane came closer to her. When he was only centimeters away from Rae, he spoke cynically, "To be honest, I don't like you _Rae_."

He grabbed her arms, pushing her into the wall harder. She tried to break free, but he was much stronger than her. Giving up, she gulped. Such an unusual man, Rae couldn't predict what he'd do next.

"And do you know what happens when I don't like someone? When they get on my _nerves_? When they _irritate_ me?"

Rae realized he was waiting for an answer. She barely shook her head to answer no.

Bane scoffed and reached into his back pocket, pulling of a sharpened pocket knife and swiftly shoving it into Rae's upper abdomen.

Bane held the knife inside her for a moment, grinning at Rae's pained expression. Finally, he slowly slid the knife from out of her and let go of her arms. She slid down the wall, holding her stomach, tears rolling down her face.

She watched as Bane sickly licked the knife clean, tasting her blood. He rolled his tongue over his teeth and grinned, showing Rae his teeth covered in her own blood. He left the mess hall, leaving Rae on the ground.

Rae looked at the wound, blood still pouring over her hands, staining her clothes and the floor. She saw the intercom, only a few meters away, and tried to get up. She cried out when she moved less than an inch.

Knowing it was the only way to warn her crewmates, her friends, she tried again, ignoring the pain. She had made it to her feet, surprisingly, and took a few steps. "Only a little further. Come on Rae, you can make it. You have to!" she urged herself.

As the pain caught up to her, she started seeing black spots, her head started to throb and her body felt woozy.

Rae started to sob when she knew she wouldn't be able to make it to the intercom. It would be her fault if Bane hurt anyone else. She had let down everyone, including her captain, including her hero. Rae completely lost her sight, only seeing black and white blobs dancing together. Her body couldn't handle it anymore and she fainted, landing hard on the ground. Less than a second later, her mind gave out too, leaving her completely helpless.

Trinity and Neo had said goodbye to all of their crewmates, except Rae and Bane. Truthfully, everyone had forgotten about Bane.

"The ship's yours whenever you're ready. I suggest you go soon though," said Niobe.

Trinity nodded.

"Do you know where Rae is?" Neo asked Morpheus.

"Yes. I sent her to the mess hall. From what I know of her, she's probably sulking in her room."

"I should go tell her we're leaving."

"Neo, you're running late. Are you sure you want to waste any more time?" Sparks questioned.

Neo looked to Trinity and back at Sparks. "You're right. The machines won't wait. Let's get moving."

Trinity followed Neo towards the Logos. She looked back once more and memorized each of her friend's faces.

"_You're being ridiculous, Trinity. You're going to see them all again. You aren't going to die, Neo's sure of that. What's going to kill you is all of your worrying!"_ Trinity scolded herself.

They had put their bags in an empty room and went into the pilot's station, buckling in and getting ready for take off. They had watched the Caduceus and the Nebuchadnezzar leave.

"Are you ready?" Neo asked.

Trinity nodded and started the ship.

Trinity piloted, as she had had much more experience than Neo did. Neo gave her directions and Trinity had followed them. They had been flying for over an hour and Trinity still had no idea where they were.

"Do you know where we're going?" she asked.

"Don't you trust me?" Neo asked. Trinity knew that meant 'yes' but decided to carry their conversation.

"Of course I do," Trinity replied

"I know."

"Then why did you ask?" she played.

Neo studied her face. Trinity looked back at him when he hadn't answered yet.

Neo couldn't keep a straight face and had smiled, making Trinity grin back.

"Captain!" Jayne yelled over the intercom. "Come down to the mess hall immediately! We have a situation!"

Both captains ran into the room. Niobe had stepped into Rae's puddle of blood on the floor. She noticed it beneath her boots and gasped, looking beside her to see Rae soaked in blood on the floor.

Morpheus' action was delayed. "What happened?" he asked.

"I don't know. We came into the mess hall and found her like this," said Jayne, looking up from the ground.

"She's still breathing, but we're going to have to get her some serious medical help," Sparks said, shedding off his sweater and tearing it in half to wrap around Rae's waist.

She was still bleeding, although it had slowed down from before.

On the count of three, Jayne, Sparks and Morpheus lifted Rae from the ground, being cautious not to irritate her wound, and carried her to the med bay.

Niobe had gone upstairs to tell the others what had happened. She then contacted the Caduceus to inform them. The two ships had landed and the Caduceus came aboard the Neb.

They met outside the med bay where Malachi, Link and Sparks were trying to stop Rae's bleeding so they could stitch up her wound.

"Do you know who did it?" Ballard asked.

"No. I trust everyone here and I know Rae wouldn't do this to herself," said Morpheus.

"It looked like she was trying to get to the intercom. Maybe to warn us." Niobe suggested.

"But to warn us about what, I do not know," said Morpheus.

"Hey, guys? Where's Bane?" Jayne asked suddenly.

Ballard looked around him and Niobe ran out of the room briefly.

"I don't think he's here," said Niobe slowly, when she came back.

"Damn! I could've sworn I saw him come in here with us!" Ballard said furiously. "Malachi, Go check our ship for Bane!"

"Kid, go with him." Morpheus ordered.

Malachi quickly washed his hands in the med bay and ran off the ship with Kid. About ten minutes later, they came back.

"We searched the entire ship, captain. We couldn't find him," said Malachi.

"Are you positive he isn't there?" Ballard asked.

"Yep."

"That must mean he's on the Logos…" said Niobe.

"Why would he be there?" Kid asked.

"Because he's Smith," said Morpheus, after a long moment.

"Just keep going straight. I'm going to check the matrix feed. I'll be right back," said Neo.

Trinity didn't reply. She looked around outside through the windshield at the unfamiliar grounds in front of her.

"Trin?"

"Oh, yeah. Go ahead," she said.

After Neo left, Trinity was still gazing out the window, amazed by the ruins of the earth.

Bane stepped quietly until he was as close to Trinity as possible, without her knowing. He watched her lean her head back and close her eyes, rubbing them gently with her hands.

Bane quickly wrapped his hand around her neck, attempting to suffocate her.

She gasped and tried to hit him from behind, but Bane had managed to dodge every hit.

"Who are you?" Trinity choked out.

"Smith," Bane answered.

Trinity started to cough. If possible, Bane's grip became tighter. Trinity began to claw at his hand.

Although she was sure she had cut him up quite a bit, his grasp didn't loosen.

She had finally managed to break free after lowering the seat and hitting him square in the face.

She avoided him as he came after her again. She had been able to run out of the room and down the ladder, yelling for Neo, until Bane jumped from the upper level down to hers, blocking her way into the next section of the ship.

"Neo!" Trinity yelled.

Thankfully, the door didn't screech when Neo opened it. Bane's back was turned against him, so he was unable to see when Neo mouthed to Trinity to hold him off for a moment while he got a weapon.

"Why are you here?" Trinity asked as Neo closed the door.

"Mr. Anderson and I have some personal conflicts we must settle. And they don't involve you."

"You aren't going to hurt him." Trinity warned.

"Oh, really? Well I think otherwise."

Bane started to move closer, but Trinity sidestepped left, keeping an equal distance.

"You'll never win, Smith."

Smith laughed. "I don't want to ruin the ending for you, so keep believing as you want."

Bane and Trinity had now moved enough that they were on opposite sides since they began. She had a choice, as always, to either continue moving so they'd be back to their original places, or turn and go through the door. Deciding to keep Neo from being surprised, and potentially getting hurt, Trinity kept moving.

This time, Bane didn't move. Trinity stopped, dangerously close to him, watching Bane smile.

They stood still for what Trinity thought, was an eternity. She prayed for Neo to come through the door any moment.

Bane surprised Trinity by yelling and attacking her. Her senses were in tune enough that she dove out of the way. Their battle soon became nearly a game of tag in the cramped room.

Neo suddenly came in, an EMP gun in his hands. Bane stopped and Trinity ran further to Neo's side.

"Are you alright?" he asked.

"Yeah, I'm fine," Trinity responded.

"Well, well, Mr. Anderson, I will say, you don't look very happy to see me." said Bane.

"Neo, it isn't Bane. Somehow Smith took over his body," Trinity warned.

"I know," replied Neo.

Trinity wasn't sure how he knew, but she decided not to question him now.

"Mr. Anderson, I don't know why you-"

"Save it!" Neo snapped. He stepped in front of Trinity and sped towards Smith, while charging the EMP gun. Neo had rammed the gun into Smith's gut and hit his face several times, though Smith didn't show any signs of weakness. On the outside, Bane's body was covered in blood and appeared bruised, but on the inside, Smith was only getting started.

Remembering there was no pilot, Trinity waited until it looked as if Neo were winning their brawl and she crossed the room, climbed up the ladder, and began to control the ship.

Once she heard a yell from Neo, she switched the ship to autopilot and hurried back to Neo. She noticed his arm; blood soaking through his fingers as he held the gash. Smith was holding a knife; probably the one that created the wound. She saw the EMP gun on the ground and figured Neo had probably dropped it when he was cut.

"Now I'm gonna kill you. Just like I killed your little friend right before you left." Smith said.

"Rae," Neo breathed.

"Oh, that was her name?"

"Why did you hurt her?" Neo asked angrily.

"I was bored. And she was merely part of a game I wanted to play," Smith answered simply.

"You're a sick bastard, you know that?" Neo said behind his teeth.

Again, Neo charged at Smith, this time hitting him much harder and tackling him to the ground. Neo smacked his face and elbowed his chest. Trinity could see nothing more but blood on Bane's appearance.

When Smith had regained himself, he pushed Neo off of him and hit his jaw. Only seconds after the punch was delivered, Trinity could see a bruise already forming.

Just as Smith was about to attack Neo again, the ship jerked and rumbled. Trinity held onto the ladder for support as Neo and Bane toppled over.

There was an extremely loud crashing sound coming from above them.

"What the hell is going on?!" Neo yelled through the noise.

The Logos was still swaying violently from side to side as Trinity climbed back up the ladder and to the pilot's station. A wild blurr of red, orange and black explosions filled the sky.

"Shit," Trinity muttered.

She hopped into one of the chairs, strapped herself in, and tried to avoid any more of the machines. She swerved left and right, her attempts fruitless.

Seeing as it was her last option, she headed up, towards the black sky. She didn't know what would happen, but thought if she could just get the machines off her tail, they'd be safe for a little while.

The ship penetrated the sky and for the first time, Trinity saw the _real_sun. A beautiful combination of pinks, yellows, blues and colors unimaginable combined around the sun. Trinity only wished Neo could see it with her.

Second later, the Logos came flying down, the power on the ship shutting down, and nothing but black ahead of them.

Trinity pumped the ignitor to start the ship again, but was too late in doing so.

They fell through the sky, crashing into a large skyscraper-like structure. Trinity heard parts of the ship collapse, fearing a part could have landed on Neo.

Once it was quiet again and all was still, she ran to Neo, finding a large amount of destruction there. Pipes were broken in half and jagged pieces of metal stuck out from the walls. She bit her lip, fearing the worst, until she saw Neo standing in the center of the room and Bane severely burned, lying on the floor next to the EMP blaster.

Light shined through into the room from a large hole in the ceiling. The sky hadn't been cleared yet and they were crashed in the center of a metal structure, so where the light came from, Trinity didn't know.

"Neo?" Trinity said, her voice coming out as a whisper.

Neo turned slowly to her. Blood was dripping down his face from a cut near his hairline.

Trinity stepped towards him cautiously, for reasons unknown. Perhaps she was afraid Neo had been taken over by Smith? Or could it be she was so surprised they had actually made it to the Machine City, _alive_, might she add, and wasn't sure how she would live on without the war she'd grown to accustomed to?

Neo also walked towards Trinity, finally closing the space in between them, hugging her and holding her for the first time in too long. Trinity began to cry into his chest and Neo kissed the top of her head.

"Trinity, are you hurt?" Neo asked.

She shook her head against him. Looking up to him and studying the scrape across his the side of his face, missing his eye by a couple centimeters. She gently ran her finger along the closing cut, stopping when Neo inhaled sharply.

"Sorry," she whispered.

"It's okay," said Neo, his voice equally soft.

"I love you, Neo," Trinity said. She sighed and buried her face into his sweater.

Neo held her tighter. "I love you, too."

They hadn't noticed when Bane stood up, blood pouring from his burns and gashes. Summoning the rest of his energy, he ran full speed into Neo's back, pushing him and Trinity into the wall behind them.

As she hit the metal, Trinity gasped.

Neo's reflexes reacted almost immediately, elbowing Bane's upper left side of his chest and punching his throat. He fell to the ground, Neo knowing he was dead for good.

He turned back to Trinity, horrified by what he saw.

Smith had pushed her into a piece of metal sticking out of the wall, impaling her through the back.

Neo removed her from the skewer and set her down on the ground.

"Trinity!" he yelled.

"Trinity, wake up!"

She groaned and opened her eyes halfway.

"Neo..."

"I'm right here," he said, taking her hand.

"You said I would live through this."

"It's my fault, Trin. It's all my fault."

"No... I don't blame you," said Trinity. "I never have... and I... never will."

Tears rolled down Neo's cheek. "Please, Trinity, don't leave me."

"I'll... never leave..." Trinity said, closing her eyes again. "Even... After I die... I'll still be with you."

"No, Trin, don't say that! You won't die. You won't, you won't, you won't."

"I... want you to... save... Zion."

"I can't. I need you to come with me," Neo said desperately.

"I can't... you know that. Please... do it for me... and Lily... even Rae."

After a moment, Neo agreed. "Alright. I'll go."

"Neo...?"

"Hm?"

"After... you win... look... at the sky."

"I will," Neo promised.

"Love... you..." Trinity whispered.

Neo saw her stop breathing. "I love you," he said, lying down next to her, sobbing.

_"You need to go now... Before it's too late."_

"I know."

_"You can beat him... I know you can... I've always had faith in you, Neo.."_

Neo stood up and walked away from Trinity's body, heading towards the ship's exit, where he then would defeat Smith and end the war for Zion... for _her_.

_"Don't ever forget me!"_

"I never could."

* * *

First off, I have to say, I'm so, so, so sorry! I haven't been able to write for a while and I hadn't realized it's been over a month since I've updated! And my usual excuse, life's been busy. To everyone who's been keeping an eye out for this chapter, I apologize.

And also, yes, I have finished Separation. But who knows, maybe I'll write a sequel!

You may have noticed I used took some of the movie's plot and morphed it into the story. If you're wondering why I did this, it's only because I really liked the Wachowski brothers' story line, so much, in fact, that I included it into mine. Also because my imagination went dead on me...

By the way, if some parts seem to be endless babble of words, it's because I haven't slept in 19 hours. I'm going to do a mass edit of the whole 18 chapters, so don't worry.

Reviews are still welcomed, as are suggestions for a sequel! :D

Lastly, an enormous thanks to anyone who has been reading/reviewing, as it means so much to me! I honestly can't thank you enough!

I hope you've all enjoyed reading Separation as much as I enjoyed writing it!

x Suicidal Imbecile


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